diff --git a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl b/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl deleted file mode 100644 index dd1d41c..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl +++ /dev/null @@ -1,2 +0,0 @@ -// once a station becomes full, probability it will be polled within T time units is ... -P=?[ true U<=10 (s=1 & a=0) ] \ No newline at end of file diff --git a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism b/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism deleted file mode 100644 index d1db524..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism +++ /dev/null @@ -1,90 +0,0 @@ -// polling example [IT90] -// gxn/dxp 26/01/00 - -ctmc - -const int N = 12; - -const double mu = 1; -const double gamma = 200; -const double lambda = mu/N; - -module server - - s : [1..N]; // station - a : [0..1]; // action: 0=polling, 1=serving - - [loop1a] (s=1)&(a=0) -> gamma : (s'=s+1); - [loop1b] (s=1)&(a=0) -> gamma : (a'=1); - [serve1] (s=1)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop2a] (s=2)&(a=0) -> gamma : (s'=s+1); - [loop2b] (s=2)&(a=0) -> gamma : (a'=1); - [serve2] (s=2)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop3a] (s=3)&(a=0) -> gamma : (s'=s+1); - [loop3b] (s=3)&(a=0) -> gamma : (a'=1); - [serve3] (s=3)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop4a] (s=4)&(a=0) -> gamma : (s'=s+1); - [loop4b] (s=4)&(a=0) -> gamma : (a'=1); - [serve4] (s=4)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop5a] (s=5)&(a=0) -> gamma : (s'=s+1); - [loop5b] (s=5)&(a=0) -> gamma : (a'=1); - [serve5] (s=5)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop6a] (s=6)&(a=0) -> gamma : (s'=s+1); - [loop6b] (s=6)&(a=0) -> gamma : (a'=1); - [serve6] (s=6)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop7a] (s=7)&(a=0) -> gamma : (s'=s+1); - [loop7b] (s=7)&(a=0) -> gamma : (a'=1); - [serve7] (s=7)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop8a] (s=8)&(a=0) -> gamma : (s'=s+1); - [loop8b] (s=8)&(a=0) -> gamma : (a'=1); - [serve8] (s=8)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop9a] (s=9)&(a=0) -> gamma : (s'=s+1); - [loop9b] (s=9)&(a=0) -> gamma : (a'=1); - [serve9] (s=9)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop10a] (s=10)&(a=0) -> gamma : (s'=s+1); - [loop10b] (s=10)&(a=0) -> gamma : (a'=1); - [serve10] (s=10)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop11a] (s=11)&(a=0) -> gamma : (s'=s+1); - [loop11b] (s=11)&(a=0) -> gamma : (a'=1); - [serve11] (s=11)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop12a] (s=12)&(a=0) -> gamma : (s'=1); - [loop12b] (s=12)&(a=0) -> gamma : (a'=1); - [serve12] (s=12)&(a=1) -> mu : (s'=1)&(a'=0); - -endmodule - -module station1 - - s1 : [0..1]; // state of station: 0=empty, 1=full - - [loop1a] (s1=0) -> 1 : (s1'=0); - [] (s1=0) -> lambda : (s1'=1); - [loop1b] (s1=1) -> 1 : (s1'=1); - [serve1] (s1=1) -> 1 : (s1'=0); - -endmodule - -// construct further stations through renaming - -module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule -module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule -module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule -module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule -module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule -module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule -module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule -module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule -module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule -module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule -module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule diff --git a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl b/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl deleted file mode 100644 index dd1d41c..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl +++ /dev/null @@ -1,2 +0,0 @@ -// once a station becomes full, probability it will be polled within T time units is ... -P=?[ true U<=10 (s=1 & a=0) ] \ No newline at end of file diff --git a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism b/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism deleted file mode 100644 index 7abe195..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism +++ /dev/null @@ -1,110 +0,0 @@ -// polling example [IT90] -// gxn/dxp 26/01/00 - -ctmc - -const int N = 16; - -const double mu = 1; -const double gamma = 200; -const double lambda = mu/N; - -module server - - s : [1..N]; // station - a : [0..1]; // action: 0=polling, 1=serving - - [loop1a] (s=1)&(a=0) -> gamma : (s'=s+1); - [loop1b] (s=1)&(a=0) -> gamma : (a'=1); - [serve1] (s=1)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop2a] (s=2)&(a=0) -> gamma : (s'=s+1); - [loop2b] (s=2)&(a=0) -> gamma : (a'=1); - [serve2] (s=2)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop3a] (s=3)&(a=0) -> gamma : (s'=s+1); - [loop3b] (s=3)&(a=0) -> gamma : (a'=1); - [serve3] (s=3)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop4a] (s=4)&(a=0) -> gamma : (s'=s+1); - [loop4b] (s=4)&(a=0) -> gamma : (a'=1); - [serve4] (s=4)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop5a] (s=5)&(a=0) -> gamma : (s'=s+1); - [loop5b] (s=5)&(a=0) -> gamma : (a'=1); - [serve5] (s=5)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop6a] (s=6)&(a=0) -> gamma : (s'=s+1); - [loop6b] (s=6)&(a=0) -> gamma : (a'=1); - [serve6] (s=6)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop7a] (s=7)&(a=0) -> gamma : (s'=s+1); - [loop7b] (s=7)&(a=0) -> gamma : (a'=1); - [serve7] (s=7)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop8a] (s=8)&(a=0) -> gamma : (s'=s+1); - [loop8b] (s=8)&(a=0) -> gamma : (a'=1); - [serve8] (s=8)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop9a] (s=9)&(a=0) -> gamma : (s'=s+1); - [loop9b] (s=9)&(a=0) -> gamma : (a'=1); - [serve9] (s=9)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop10a] (s=10)&(a=0) -> gamma : (s'=s+1); - [loop10b] (s=10)&(a=0) -> gamma : (a'=1); - [serve10] (s=10)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop11a] (s=11)&(a=0) -> gamma : (s'=s+1); - [loop11b] (s=11)&(a=0) -> gamma : (a'=1); - [serve11] (s=11)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop12a] (s=12)&(a=0) -> gamma : (s'=s+1); - [loop12b] (s=12)&(a=0) -> gamma : (a'=1); - [serve12] (s=12)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop13a] (s=13)&(a=0) -> gamma : (s'=s+1); - [loop13b] (s=13)&(a=0) -> gamma : (a'=1); - [serve13] (s=13)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop14a] (s=14)&(a=0) -> gamma : (s'=s+1); - [loop14b] (s=14)&(a=0) -> gamma : (a'=1); - [serve14] (s=14)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop15a] (s=15)&(a=0) -> gamma : (s'=s+1); - [loop15b] (s=15)&(a=0) -> gamma : (a'=1); - [serve15] (s=15)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop16a] (s=16)&(a=0) -> gamma : (s'=1); - [loop16b] (s=16)&(a=0) -> gamma : (a'=1); - [serve16] (s=16)&(a=1) -> mu : (s'=1)&(a'=0); - -endmodule - -module station1 - - s1 : [0..1]; // state of station: 0=empty, 1=full - - [loop1a] (s1=0) -> 1 : (s1'=0); - [] (s1=0) -> lambda : (s1'=1); - [loop1b] (s1=1) -> 1 : (s1'=1); - [serve1] (s1=1) -> 1 : (s1'=0); - -endmodule - -// construct further stations through renaming - -module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule -module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule -module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule -module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule -module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule -module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule -module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule -module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule -module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule -module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule -module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule -module station13 = station1 [ s1=s13, loop1a=loop13a, loop1b=loop13b, serve1=serve13 ] endmodule -module station14 = station1 [ s1=s14, loop1a=loop14a, loop1b=loop14b, serve1=serve14 ] endmodule -module station15 = station1 [ s1=s15, loop1a=loop15a, loop1b=loop15b, serve1=serve15 ] endmodule -module station16 = station1 [ s1=s16, loop1a=loop16a, loop1b=loop16b, serve1=serve16 ] endmodule diff --git a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl b/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl deleted file mode 100644 index dd1d41c..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl +++ /dev/null @@ -1,2 +0,0 @@ -// once a station becomes full, probability it will be polled within T time units is ... -P=?[ true U<=10 (s=1 & a=0) ] \ No newline at end of file diff --git a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism b/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism deleted file mode 100644 index bee0591..0000000 --- a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism +++ /dev/null @@ -1,130 +0,0 @@ -// polling example [IT90] -// gxn/dxp 26/01/00 - -ctmc - -const int N = 20; - -const double mu = 1; -const double gamma = 200; -const double lambda = mu/N; - -module server - - s : [1..N]; // station - a : [0..1]; // action: 0=polling, 1=serving - - [loop1a] (s=1)&(a=0) -> gamma : (s'=s+1); - [loop1b] (s=1)&(a=0) -> gamma : (a'=1); - [serve1] (s=1)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop2a] (s=2)&(a=0) -> gamma : (s'=s+1); - [loop2b] (s=2)&(a=0) -> gamma : (a'=1); - [serve2] (s=2)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop3a] (s=3)&(a=0) -> gamma : (s'=s+1); - [loop3b] (s=3)&(a=0) -> gamma : (a'=1); - [serve3] (s=3)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop4a] (s=4)&(a=0) -> gamma : (s'=s+1); - [loop4b] (s=4)&(a=0) -> gamma : (a'=1); - [serve4] (s=4)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop5a] (s=5)&(a=0) -> gamma : (s'=s+1); - [loop5b] (s=5)&(a=0) -> gamma : (a'=1); - [serve5] (s=5)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop6a] (s=6)&(a=0) -> gamma : (s'=s+1); - [loop6b] (s=6)&(a=0) -> gamma : (a'=1); - [serve6] (s=6)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop7a] (s=7)&(a=0) -> gamma : (s'=s+1); - [loop7b] (s=7)&(a=0) -> gamma : (a'=1); - [serve7] (s=7)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop8a] (s=8)&(a=0) -> gamma : (s'=s+1); - [loop8b] (s=8)&(a=0) -> gamma : (a'=1); - [serve8] (s=8)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop9a] (s=9)&(a=0) -> gamma : (s'=s+1); - [loop9b] (s=9)&(a=0) -> gamma : (a'=1); - [serve9] (s=9)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop10a] (s=10)&(a=0) -> gamma : (s'=s+1); - [loop10b] (s=10)&(a=0) -> gamma : (a'=1); - [serve10] (s=10)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop11a] (s=11)&(a=0) -> gamma : (s'=s+1); - [loop11b] (s=11)&(a=0) -> gamma : (a'=1); - [serve11] (s=11)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop12a] (s=12)&(a=0) -> gamma : (s'=s+1); - [loop12b] (s=12)&(a=0) -> gamma : (a'=1); - [serve12] (s=12)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop13a] (s=13)&(a=0) -> gamma : (s'=s+1); - [loop13b] (s=13)&(a=0) -> gamma : (a'=1); - [serve13] (s=13)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop14a] (s=14)&(a=0) -> gamma : (s'=s+1); - [loop14b] (s=14)&(a=0) -> gamma : (a'=1); - [serve14] (s=14)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop15a] (s=15)&(a=0) -> gamma : (s'=s+1); - [loop15b] (s=15)&(a=0) -> gamma : (a'=1); - [serve15] (s=15)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop16a] (s=16)&(a=0) -> gamma : (s'=s+1); - [loop16b] (s=16)&(a=0) -> gamma : (a'=1); - [serve16] (s=16)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop17a] (s=17)&(a=0) -> gamma : (s'=s+1); - [loop17b] (s=17)&(a=0) -> gamma : (a'=1); - [serve17] (s=17)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop18a] (s=18)&(a=0) -> gamma : (s'=s+1); - [loop18b] (s=18)&(a=0) -> gamma : (a'=1); - [serve18] (s=18)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop19a] (s=19)&(a=0) -> gamma : (s'=s+1); - [loop19b] (s=19)&(a=0) -> gamma : (a'=1); - [serve19] (s=19)&(a=1) -> mu : (s'=s+1)&(a'=0); - - [loop20a] (s=20)&(a=0) -> gamma : (s'=1); - [loop20b] (s=20)&(a=0) -> gamma : (a'=1); - [serve20] (s=20)&(a=1) -> mu : (s'=1)&(a'=0); - -endmodule - -module station1 - - s1 : [0..1]; // state of station: 0=empty, 1=full - - [loop1a] (s1=0) -> 1 : (s1'=0); - [] (s1=0) -> lambda : (s1'=1); - [loop1b] (s1=1) -> 1 : (s1'=1); - [serve1] (s1=1) -> 1 : (s1'=0); - -endmodule - -// construct further stations through renaming - -module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule -module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule -module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule -module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule -module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule -module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule -module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule -module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule -module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule -module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule -module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule -module station13 = station1 [ s1=s13, loop1a=loop13a, loop1b=loop13b, serve1=serve13 ] endmodule -module station14 = station1 [ s1=s14, loop1a=loop14a, loop1b=loop14b, serve1=serve14 ] endmodule -module station15 = station1 [ s1=s15, loop1a=loop15a, loop1b=loop15b, serve1=serve15 ] endmodule -module station16 = station1 [ s1=s16, loop1a=loop16a, loop1b=loop16b, serve1=serve16 ] endmodule -module station17 = station1 [ s1=s17, loop1a=loop17a, loop1b=loop17b, serve1=serve17 ] endmodule -module station18 = station1 [ s1=s18, loop1a=loop18a, loop1b=loop18b, serve1=serve18 ] endmodule -module station19 = station1 [ s1=s19, loop1a=loop19a, loop1b=loop19b, serve1=serve19 ] endmodule -module station20 = station1 [ s1=s20, loop1a=loop20a, loop1b=loop20b, serve1=serve20 ] endmodule diff --git a/Benchmarks/PRISM/README.md b/Benchmarks/PRISM/README.md deleted file mode 100644 index 9c1f3e3..0000000 --- a/Benchmarks/PRISM/README.md +++ /dev/null @@ -1,20 +0,0 @@ -# PRISM Benchmarks - -Some benchmarks here were taken from those provided by [PRISM](https://prismmodelchecker.org). The upstream URL is [https://github.com/prismmodelchecker/prism-benchmarks](https://github.com/prismmodelchecker/prism-benchmarks). - -## Jackson - -TODO: Steal description from PRISM folks - -## Polling - -TODO: Steal description from PRISM folks - -## Robot World - -TODO: Steal description from PRISM folks - -## Tandem Queue - -TODO: Steal description from PRISM folks - diff --git a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.jani new file mode 100644 index 0000000..5097a38 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.jani @@ -0,0 +1,299 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00001-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props index 9662c48..3cc4dd8 100644 --- a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00001/00001-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm index 0cd09ca..fa96c67 100644 --- a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00001/results.txt b/Benchmarks/SBMLstochasticTests/00001/results.txt new file mode 100644 index 0000000..522462f --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00001/results.txt @@ -0,0 +1,2 @@ +0.6725212076689461 +0.6732478300215641 diff --git a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.jani new file mode 100644 index 0000000..21d5ad2 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.jani @@ -0,0 +1,299 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "local_Lambda_0", + "type": "real", + "value": 0.1 + }, + { + "name": "local_Mu_1", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00002-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props index 8fb482f..7c139c3 100644 --- a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00002/00002-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm index 03be53e..7a65479 100644 --- a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model local parameters -const double local_Lambda_0 = 0.1; // -const double local_Mu_1 = 0.11; // +const double local_Lambda_0 = 0.1; // +const double local_Mu_1 = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (local_Lambda_0 * _X) > 0 -> (local_Lambda_0 * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (local_Mu_1 * _X) > 0 -> (local_Mu_1 * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.jani new file mode 100644 index 0000000..ede1afc --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.jani @@ -0,0 +1,299 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1 * _X) / (1 * _X))", + "exp": { + "left": { + "left": 1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1 * _X) > 0)", + "exp": { + "left": { + "left": 1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1 * _X)", + "exp": { + "left": 1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/10 * _X) / (11/10 * _X))", + "exp": { + "left": { + "left": 1.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 1.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/10 * _X) > 0)", + "exp": { + "left": { + "left": 1.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/10 * _X)", + "exp": { + "left": 1.1, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 1.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00003-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 0.67379 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props index a7584e6..3a0c431 100644 --- a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00003/00003-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 0.67379) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 0.67379) ] diff --git a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm index b3fe59d..83364bf 100644 --- a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 1.0; // -const double Mu = 1.1; // +const double Lambda = 1.0; // +const double Mu = 1.1; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.jani new file mode 100644 index 0000000..c4083ff --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.jani @@ -0,0 +1,299 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00004-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 6.06531 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 10, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props index 30b1078..83667e4 100644 --- a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00004/00004-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 6.06531) ] \ No newline at end of file +P=? [true U[0,50] (_X < 6.06531) ] diff --git a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm index 763c39e..b01e4a7 100644 --- a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm @@ -1,5 +1,5 @@ // File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00004/00004-sbml-l3v2.xml +// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.xml // @GeneticLogicLab ctmc @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 10; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -25,10 +25,10 @@ endmodule // Reaction rates module reaction_rates - // Birth: -> _X -> _X + // Birth: _X -> _X // 2 [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00004/results.txt b/Benchmarks/SBMLstochasticTests/00004/results.txt new file mode 100644 index 0000000..0c72a40 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00004/results.txt @@ -0,0 +1,2 @@ +0.8511625487681788 +0.8515501349900346 diff --git a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.jani new file mode 100644 index 0000000..cce2e88 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.jani @@ -0,0 +1,299 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00005-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 6065.307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 10000, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props index 84d3d24..ae1dc31 100644 --- a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00005/00005-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 6065.307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 6065.307) ] diff --git a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm index a50e6be..d7baaeb 100644 --- a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 10000; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00005/results.txt b/Benchmarks/SBMLstochasticTests/00005/results.txt new file mode 100644 index 0000000..61aabea --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00005/results.txt @@ -0,0 +1,2 @@ +0.0 +0.9999999999999412 diff --git a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.jani new file mode 100644 index 0000000..9ff9594 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.jani @@ -0,0 +1,370 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + }, + { + "comment": "rewardmodel_Sink <- Sink", + "ref": "rewardmodel_Sink", + "value": "Sink" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "Sink <- (Sink + 1)", + "ref": "Sink", + "value": { + "left": "Sink", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(Sink >= 0)", + "exp": { + "left": "Sink", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Sink", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00006-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "Sink" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + null, + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Sink", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + }, + { + "initial-value": 0, + "name": "Sink", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props index 7bae58e..0695513 100644 --- a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00006/00006-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm index 4875077..f2912df 100644 --- a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module Sink Sink : int init 0; // Death - [Death] Sink > 0 -> (Sink' = Sink + 1); + [Death] Sink >= 0 -> (Sink' = Sink + 1); endmodule diff --git a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.jani new file mode 100644 index 0000000..42a6aa8 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.jani @@ -0,0 +1,370 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + }, + { + "comment": "rewardmodel_Sink <- Sink", + "ref": "rewardmodel_Sink", + "value": "Sink" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "Sink <- (Sink + 1)", + "ref": "Sink", + "value": { + "left": "Sink", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(Sink >= 0)", + "exp": { + "left": "Sink", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Sink", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00007-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "Sink" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + null, + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Sink", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + }, + { + "initial-value": 0, + "name": "Sink", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props index 8116f74..ce97fa1 100644 --- a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00007/00007-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm index 3f31f1b..cdd4b47 100644 --- a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module Sink Sink : int init 0; // Death - [Death] Sink > 0 -> (Sink' = Sink + 1); + [Death] Sink >= 0 -> (Sink' = Sink + 1); endmodule diff --git a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.jani new file mode 100644 index 0000000..5c7e772 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 1 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00008-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props index 3f2f2b5..ef2e2d3 100644 --- a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00008/00008-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm index ad47519..bda5c68 100644 --- a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 1.0; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.jani new file mode 100644 index 0000000..0172083 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 2 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00009-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props index 0e7a2a7..05c8ba7 100644 --- a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00009/00009-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm index d470225..bc01e2d 100644 --- a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 2.0; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.jani new file mode 100644 index 0000000..7777d58 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 1 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00010-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props index a4cd534..c5d154d 100644 --- a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00010/00010-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm index e644b67..e6a8b70 100644 --- a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 1.0; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.jani new file mode 100644 index 0000000..8e68403 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 2 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00011-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "≤", + "right": 20 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props index 6b42849..b50a47f 100644 --- a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00011/00011-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 77.88008) ] \ No newline at end of file +P=? [ true U [0,50] (_X <= 20) ] diff --git a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm index 4700709..32dfaed 100644 --- a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 2.0; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.jani new file mode 100644 index 0000000..06c728c --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.jani @@ -0,0 +1,331 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((((1/10 * _X) * 1/2) * 2) / (((1/10 * _X) * 1/2) * 2))", + "exp": { + "left": { + "left": { + "left": 2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": { + "left": 0.5, + "op": "*", + "right": 0.1 + } + }, + "op": "/", + "right": { + "left": { + "left": 2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": { + "left": 0.5, + "op": "*", + "right": 0.1 + } + } + } + } + } + ], + "guard": { + "comment": "((((1/10 * _X) * 1/2) * 2) > 0)", + "exp": { + "left": { + "left": { + "left": 2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": { + "left": 0.5, + "op": "*", + "right": 0.1 + } + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(((1/10 * _X) * 1/2) * 2)", + "exp": { + "left": { + "left": 2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": { + "left": 0.5, + "op": "*", + "right": 0.1 + } + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00012-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props index 04a649c..331d92a 100644 --- a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00012/00012-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm index c681204..362693b 100644 --- a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X* 0.5 * 2) > 0 -> (Lambda * _X* 0.5 * 2) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.jani new file mode 100644 index 0000000..c996705 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.jani @@ -0,0 +1,315 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1/5 * _X) * 1/2) / ((1/5 * _X) * 1/2))", + "exp": { + "left": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": 0.5 + }, + "op": "/", + "right": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": 0.5 + } + } + } + } + ], + "guard": { + "comment": "(((1/5 * _X) * 1/2) > 0)", + "exp": { + "left": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": 0.5 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1/5 * _X) * 1/2)", + "exp": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": "*", + "right": 0.5 + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.2 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00013-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props index 70fb0f1..81bc885 100644 --- a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00013/00013-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm index 1dad711..9a1fdfe 100644 --- a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.2; // -const double Mu = 0.11; // +const double Lambda = 0.2; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X* 0.5) > 0 -> (Lambda * _X* 0.5) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.jani new file mode 100644 index 0000000..7c93099 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.jani @@ -0,0 +1,331 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((((1/10 * _X) / 2) / 1/2) / (((1/10 * _X) / 2) / 1/2))", + "exp": { + "left": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": 0.5 + }, + "op": "/", + "right": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": 0.5 + } + } + } + } + ], + "guard": { + "comment": "((((1/10 * _X) / 2) / 1/2) > 0)", + "exp": { + "left": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": 0.5 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(((1/10 * _X) / 2) / 1/2)", + "exp": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": 0.5 + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00014-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props index 3da903c..9e03f4a 100644 --- a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00014/00014-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm index 943151a..47e3739 100644 --- a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (((Lambda * _X) / 2) / 0.5) > 0 -> (((Lambda * _X) / 2) / 0.5) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.jani new file mode 100644 index 0000000..73dc56d --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.jani @@ -0,0 +1,331 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1/10 * (_X / 2)) / 1/2) / ((1/10 * (_X / 2)) / 1/2))", + "exp": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": { + "left": "_X", + "op": "/", + "right": 2 + } + }, + "op": "/", + "right": 0.5 + }, + "op": "/", + "right": { + "left": { + "left": 0.1, + "op": "*", + "right": { + "left": "_X", + "op": "/", + "right": 2 + } + }, + "op": "/", + "right": 0.5 + } + } + } + } + ], + "guard": { + "comment": "(((1/10 * (_X / 2)) / 1/2) > 0)", + "exp": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": { + "left": "_X", + "op": "/", + "right": 2 + } + }, + "op": "/", + "right": 0.5 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1/10 * (_X / 2)) / 1/2)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": { + "left": "_X", + "op": "/", + "right": 2 + } + }, + "op": "/", + "right": 0.5 + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00015-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props index 83f34b8..e0caad0 100644 --- a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00015/00015-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm index 4226cd3..fe6bf66 100644 --- a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] ((Lambda * ( _X/ 2)) / 0.5) > 0 -> ((Lambda * ( _X/ 2)) / 0.5) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.jani new file mode 100644 index 0000000..bab2302 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.jani @@ -0,0 +1,315 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1/10 * _X) / (2 / 2)) / ((1/10 * _X) / (2 / 2)))", + "exp": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 1 + }, + "op": "/", + "right": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 1 + } + } + } + } + ], + "guard": { + "comment": "(((1/10 * _X) / (2 / 2)) > 0)", + "exp": { + "left": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 1 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1/10 * _X) / (2 / 2))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": 1 + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00016-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props index 497063c..f5bdb17 100644 --- a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00016/00016-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm index 0c79e66..c7f06e0 100644 --- a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] ((Lambda * _X) / (2 / 2)) > 0 -> ((Lambda * _X) / (2 / 2)) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.jani new file mode 100644 index 0000000..33deb35 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1 * 1/10) * _X) / ((1 * 1/10) * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "(((1 * 1/10) * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1 * 1/10) * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1 * 11/100) * _X) / ((1 * 11/100) * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "(((1 * 11/100) * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1 * 11/100) * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 1 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00017-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props index 7ce43b8..68b7ce6 100644 --- a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00017/00017-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm index d0f37c5..28db085 100644 --- a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 1.0; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Cell * Lambda * _X) > 0 -> (Cell * Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Cell * Mu * _X) > 0 -> (Cell * Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.jani new file mode 100644 index 0000000..4e56eca --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.jani @@ -0,0 +1,304 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1/2 * 1/10) * _X) / ((1/2 * 1/10) * _X))", + "exp": { + "left": { + "left": 0.05, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.05, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "(((1/2 * 1/10) * _X) > 0)", + "exp": { + "left": { + "left": 0.05, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1/2 * 1/10) * _X)", + "exp": { + "left": 0.05, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((1/2 * 11/100) * _X) / ((1/2 * 11/100) * _X))", + "exp": { + "left": { + "left": 0.055, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.055, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "(((1/2 * 11/100) * _X) > 0)", + "exp": { + "left": { + "left": 0.055, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((1/2 * 11/100) * _X)", + "exp": { + "left": 0.055, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Cell", + "type": "real", + "value": 0.5 + }, + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00018-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 77.88008 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props index d30c4ca..465e9c3 100644 --- a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00018/00018-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 77.88008) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 77.88008) ] diff --git a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm index 25e19d0..57a8600 100644 --- a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm @@ -8,8 +8,8 @@ ctmc const double Cell = 0.5; // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -17,7 +17,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -29,7 +29,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Cell * Lambda * _X) > 0 -> (Cell * Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Cell * Mu * _X) > 0 -> (Cell * Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.jani new file mode 100644 index 0000000..2aa146f --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.jani @@ -0,0 +1,333 @@ +{ + "actions": [ + { + "name": "Birth" + }, + { + "name": "Death" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + }, + { + "comment": "rewardmodel_y <- y", + "ref": "rewardmodel_y", + "value": "y" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "y", + "variables": [] + }, + { + "edges": [ + { + "action": "Birth", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((11/100 * _X) / (11/100 * _X))", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((11/100 * _X) > 0)", + "exp": { + "left": { + "left": 0.11, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(11/100 * _X)", + "exp": { + "left": 0.11, + "op": "*", + "right": "_X" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Lambda", + "type": "real", + "value": 0.1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.11 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00019-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 60.65307 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "y" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Birth", + "synchronise": [ + "Birth", + null, + "Birth" + ] + }, + { + "result": "Death", + "synchronise": [ + "Death", + null, + "Death" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_y", + "transient": true, + "type": "real" + }, + { + "initial-value": 100, + "name": "_X", + "type": "int" + }, + { + "initial-value": 0, + "name": "y", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props index 70ad67d..3e678f6 100644 --- a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00019/00019-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 60.65307) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 60.65307) ] diff --git a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm index 3122cb9..f34ff10 100644 --- a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Lambda = 0.1; // -const double Mu = 0.11; // +const double Lambda = 0.1; // +const double Mu = 0.11; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 100; // Birth - [Birth] _X > 0 -> (_X' = _X + 1); + [Birth] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -36,7 +36,7 @@ module reaction_rates // Birth: -> _X -> _X [Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.jani new file mode 100644 index 0000000..d1be763 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00020-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": ">", + "right": 9.93262 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props index 76ed6d5..ea20172 100644 --- a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00020/00020-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 9.93262) ] \ No newline at end of file +P=? [ true U [0,50] (_X > 9.93262) ] diff --git a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm index 22d2dad..c4e3cea 100644 --- a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 0.1; // +const double Alpha = 1.0; // +const double Mu = 0.1; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.jani new file mode 100644 index 0000000..f8dde7a --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(10 / 10)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(10 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "10", + "exp": 10 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 10 + }, + { + "name": "Mu", + "type": "real", + "value": 0.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00021-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": ">", + "right": 99.3262 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props index 035426b..02b0248 100644 --- a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00021/00021-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 99.3262) ] \ No newline at end of file +P=? [ true U [0,50] (_X > 99.3262) ] diff --git a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm index 90457ef..2bf7229 100644 --- a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 10.0; // -const double Mu = 0.1; // +const double Alpha = 10.0; // +const double Mu = 0.1; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00021/results.txt b/Benchmarks/SBMLstochasticTests/00021/results.txt new file mode 100644 index 0000000..b2dc1ea --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00021/results.txt @@ -0,0 +1,2 @@ +0.0 +0.0 diff --git a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.jani new file mode 100644 index 0000000..55791e5 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.jani @@ -0,0 +1,280 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(5 / 5)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(5 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "5", + "exp": 5 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 10 + }, + { + "name": "Mu", + "type": "real", + "value": 0.1 + }, + { + "name": "local_Alpha_0", + "type": "real", + "value": 5 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00022-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": ">", + "right": 49.6631 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props index 4c66ad6..d828aa1 100644 --- a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00022/00022-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 49.6631) ] \ No newline at end of file +P=? [ true U [0,50] (_X > 49.6631) ] diff --git a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm index 9b8ebc7..b140861 100644 --- a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm @@ -7,11 +7,11 @@ ctmc // Compartment size // Model parameters -const double Alpha = 10.0; // -const double Mu = 0.1; // +const double Alpha = 10.0; // +const double Mu = 0.1; // // Model local parameters -const double local_Alpha_0 = 5.0; // +const double local_Alpha_0 = 5.0; // // Species _X module _X @@ -19,7 +19,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -31,7 +31,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] local_Alpha_0 > 0 -> local_Alpha_0 : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props deleted file mode 100644 index d40963b..0000000 --- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00023/00023-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X > 9932.62) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm deleted file mode 100644 index 0ed4f14..0000000 --- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm +++ /dev/null @@ -1,38 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00023/00023-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double Alpha = 1000.0; // -const double Mu = 0.1; // - -// Species _X -module _X - - _X : int init 0; - - // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); - // Death - [Death] _X > 0 -> (_X' = _X - 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Immigration: -> -> _X - [Immigration] Alpha > 0 -> Alpha : true; - - // Death: -> _X -> - [Death] (Mu * _X) > 0 -> (Mu * _X) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml deleted file mode 100755 index 89af29b..0000000 --- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml +++ /dev/null @@ -1,41 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - Alpha - - - - - - - - - - - - Mu - X - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props deleted file mode 100644 index 3c6ef61..0000000 --- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00024/00024-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X > 99.3262) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm deleted file mode 100644 index 90b352e..0000000 --- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm +++ /dev/null @@ -1,62 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00024/00024-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double Alpha = 10.0; // -const double Mu = 0.1; // - -// Species _X -module _X - - _X : int init 0; - - // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); - // Death - [Death] _X > 0 -> (_X' = _X - 1); - -endmodule - -// Species Source -module Source - - Source : int init 0; - - // Immigration - [Immigration] Source > 0 -> (Source' = Source - 1); - -endmodule - -// Species Sink -module Sink - - Sink : int init 0; - - // Death - [Death] Sink > 0 -> (Sink' = Sink + 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Immigration: -> Source -> _X - [Immigration] Alpha > 0 -> Alpha : true; - - // Death: -> _X -> Sink - [Death] (Mu * _X) > 0 -> (Mu * _X) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards -// Reward 2: Source -rewards "Source" true : Source; endrewards -// Reward 3: Sink -rewards "Sink" true : Sink; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml deleted file mode 100755 index 4136c9f..0000000 --- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - Alpha - - - - - - - - - - - - - - - Mu - X - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props deleted file mode 100644 index 0438bbd..0000000 --- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00025/00025-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X > 99.3262) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm deleted file mode 100644 index 397f904..0000000 --- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm +++ /dev/null @@ -1,62 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00025/00025-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double Alpha = 10.0; // -const double Mu = 0.1; // - -// Species _X -module _X - - _X : int init 0; - - // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); - // Death - [Death] _X > 0 -> (_X' = _X - 1); - -endmodule - -// Species Source -module Source - - Source : int init 0; - - // Immigration - [Immigration] Source > 0 -> (Source' = Source - 1); - -endmodule - -// Species Sink -module Sink - - Sink : int init 0; - - // Death - [Death] Sink > 0 -> (Sink' = Sink + 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Immigration: -> Source -> _X - [Immigration] Alpha > 0 -> Alpha : true; - - // Death: -> _X -> Sink - [Death] (Mu * _X) > 0 -> (Mu * _X) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards -// Reward 2: Source -rewards "Source" true : Source; endrewards -// Reward 3: Sink -rewards "Sink" true : Sink; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml deleted file mode 100755 index d0460f6..0000000 --- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - Alpha - - - - - - - - - - - - - - - Mu - X - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props deleted file mode 100644 index 82473ca..0000000 --- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00026/00026-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X > 99.3262) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm deleted file mode 100644 index 8d09353..0000000 --- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm +++ /dev/null @@ -1,62 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00026/00026-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double Alpha = 10.0; // -const double Mu = 0.1; // - -// Species _X -module _X - - _X : int init 0; - - // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); - // Death - [Death] _X > 0 -> (_X' = _X - 1); - -endmodule - -// Species Source -module Source - - Source : int init 0; - - // Immigration - [Immigration] Source > 0 -> (Source' = Source - 1); - -endmodule - -// Species Sink -module Sink - - Sink : int init 0; - - // Death - [Death] Sink > 0 -> (Sink' = Sink + 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Immigration: -> Source -> _X - [Immigration] Alpha > 0 -> Alpha : true; - - // Death: -> _X -> Sink - [Death] (Mu * _X) > 0 -> (Mu * _X) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards -// Reward 2: Source -rewards "Source" true : Source; endrewards -// Reward 3: Sink -rewards "Sink" true : Sink; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml deleted file mode 100755 index 22e15cb..0000000 --- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml +++ /dev/null @@ -1,49 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - Alpha - - - - - - - - - - - - - - - Mu - X - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.jani new file mode 100644 index 0000000..d78bbc9 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.jani @@ -0,0 +1,280 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "k", + "type": "real", + "value": 2 + }, + { + "name": "local_k_0", + "type": "real", + "value": 1 + }, + { + "name": "local_k_1", + "type": "real", + "value": 0.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00027-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": ">", + "right": 9.93262 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props index 23d31a7..bd8202f 100644 --- a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00027/00027-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 9.93262) ] \ No newline at end of file +P=? [ true U [0,50] (_X > 9.93262) ] diff --git a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm index cac6195..21da14d 100644 --- a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm @@ -7,11 +7,11 @@ ctmc // Compartment size // Model parameters -const double k = 2.0; // +const double k = 2.0; // // Model local parameters -const double local_k_0 = 1.0; // -const double local_k_1 = 0.1; // +const double local_k_0 = 1.0; // +const double local_k_1 = 0.1; // // Species _X module _X @@ -19,7 +19,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -31,7 +31,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] local_k_0 > 0 -> local_k_0 : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (local_k_1 * _X) > 0 -> (local_k_1 * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00027/results.txt b/Benchmarks/SBMLstochasticTests/00027/results.txt new file mode 100644 index 0000000..b30237d --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00027/results.txt @@ -0,0 +1,2 @@ +0.981591707975164 +0.981591707975164 diff --git a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.jani new file mode 100644 index 0000000..e864501 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00028-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 13.283399945 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props index 6cd5888..19c8a50 100644 --- a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00028/00028-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 13.283399945) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 13.283399945) ] diff --git a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm index f9298d3..f940ba8 100644 --- a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 0.1; // +const double Alpha = 1.0; // +const double Mu = 0.1; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.jani new file mode 100644 index 0000000..b6412cb --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/10 * _X) / (1/10 * _X))", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/10 * _X) > 0)", + "exp": { + "left": { + "left": 0.1, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/10 * _X)", + "exp": { + "left": 0.1, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.1 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00029-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "<", + "right": 10.6392786121 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props index b4089ff..eed452c 100644 --- a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00029/00029-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X < 10.6392786121) ] \ No newline at end of file +P=? [ true U [0,50] (_X < 10.6392786121) ] diff --git a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm index aaad123..fd9926e 100644 --- a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 0.1; // +const double Alpha = 1.0; // +const double Mu = 0.1; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 1); + [Immigration] _X >= 0 -> (_X' = _X + 1); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props deleted file mode 100644 index a163091..0000000 --- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00030/00030-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X < 28.542298) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm deleted file mode 100644 index b5321f9..0000000 --- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm +++ /dev/null @@ -1,52 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00030/00030-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // - -// Species _P -module _P - - _P : int init 100; - - // Dimerisation - [Dimerisation] _P > 0 -> (_P' = _P - 2); - // Disassociation - [Disassociation] _P > 0 -> (_P' = _P + 2); - -endmodule - -// Species P2 -module P2 - - P2 : int init 0; - - // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); - // Disassociation - [Disassociation] P2 > 0 -> (P2' = P2 - 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Dimerisation: -> _P -> P2 - [Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true; - - // Disassociation: -> P2 -> _P - [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _P -rewards "_P" true : _P; endrewards -// Reward 2: P2 -rewards "P2" true : P2; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml deleted file mode 100755 index 52c5718..0000000 --- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k1 - P - - - P - 1 - - - 2 - - - - - - - - - - - - - - - - k2 - P2 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props deleted file mode 100644 index 8820a70..0000000 --- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00031/00031-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X < 144.995965) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm deleted file mode 100644 index 79534c0..0000000 --- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm +++ /dev/null @@ -1,52 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00031/00031-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double k1 = 2.0E-4; // -const double k2 = 0.004; // - -// Species _P -module _P - - _P : int init 1000; - - // Dimerisation - [Dimerisation] _P > 0 -> (_P' = _P - 2); - // Disassociation - [Disassociation] _P > 0 -> (_P' = _P + 2); - -endmodule - -// Species P2 -module P2 - - P2 : int init 0; - - // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); - // Disassociation - [Disassociation] P2 > 0 -> (P2' = P2 - 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Dimerisation: -> _P -> P2 - [Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true; - - // Disassociation: -> P2 -> _P - [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _P -rewards "_P" true : _P; endrewards -// Reward 2: P2 -rewards "P2" true : P2; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml deleted file mode 100755 index 1b978f8..0000000 --- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k1 - P - - - P - 1 - - - 2 - - - - - - - - - - - - - - - - k2 - P2 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props deleted file mode 100644 index 4d8bd18..0000000 --- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00032/00032-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X < 34.887453) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm deleted file mode 100644 index 5351e6e..0000000 --- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm +++ /dev/null @@ -1,52 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00032/00032-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // - -// Species _P -module _P - - _P : int init 100; - - // Dimerisation - [Dimerisation] _P > 0 -> (_P' = _P - 2); - // Disassociation - [Disassociation] _P > 0 -> (_P' = _P + 2); - -endmodule - -// Species P2 -module P2 - - P2 : int init 0; - - // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); - // Disassociation - [Disassociation] P2 > 0 -> (P2' = P2 - 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Dimerisation: -> _P -> P2 - [Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true; - - // Disassociation: -> P2 -> _P - [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _P -rewards "_P" true : _P; endrewards -// Reward 2: P2 -rewards "P2" true : P2; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml deleted file mode 100755 index 7ba81c8..0000000 --- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k1 - P - - - P - 1 - - - 2 - - - - - - - - - - - - - - - - k2 - P2 - - - - - - - - - - - - t - 25 - - - - - - - 100 - - - - - 0 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props deleted file mode 100644 index af5c237..0000000 --- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00033/00033-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X > 58.3027904) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm deleted file mode 100644 index bdb0ba6..0000000 --- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm +++ /dev/null @@ -1,52 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00033/00033-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size - -// Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // - -// Species _P -module _P - - _P : int init 100; - - // Dimerisation - [Dimerisation] _P > 0 -> (_P' = _P - 2); - // Disassociation - [Disassociation] _P > 0 -> (_P' = _P + 2); - -endmodule - -// Species P2 -module P2 - - P2 : int init 0; - - // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); - // Disassociation - [Disassociation] P2 > 0 -> (P2' = P2 - 1); - -endmodule - -// Reaction rates -module reaction_rates - - // Dimerisation: -> _P -> P2 - [Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true; - - // Disassociation: -> P2 -> _P - [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: _P -rewards "_P" true : _P; endrewards -// Reward 2: P2 -rewards "P2" true : P2; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml deleted file mode 100755 index 5023e4a..0000000 --- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml +++ /dev/null @@ -1,86 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - k1 - P - - - P - 1 - - - 2 - - - - - - - - - - - - - - - - k2 - P2 - - - - - - - - - - - - P2 - 30 - - - - - - - 100 - - - - - 0 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.jani new file mode 100644 index 0000000..be6a194 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.jani @@ -0,0 +1,379 @@ +{ + "actions": [ + { + "name": "Dimerisation" + }, + { + "name": "Disassociation" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 + 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 >= 0)", + "exp": { + "left": "P2", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 - 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 > 0)", + "exp": { + "left": "P2", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_P2 <- P2", + "ref": "rewardmodel_P2", + "value": "P2" + } + ] + } + ], + "name": "P2", + "variables": [] + }, + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((((1/2 * 1/1000) * (100 - (2 * P2))) * (99 - (2 * P2))) / (((1/2 * 1/1000) * (100 - (2 * P2))) * (99 - (2 * P2))))", + "exp": { + "left": { + "left": { + "left": 0.0005, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": 99, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "/", + "right": { + "left": { + "left": 0.0005, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": 99, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + } + } + } + } + ], + "guard": { + "comment": "((((1/2 * 1/1000) * (100 - (2 * P2))) * (99 - (2 * P2))) > 0)", + "exp": { + "left": { + "left": { + "left": 0.0005, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": 99, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(((1/2 * 1/1000) * (100 - (2 * P2))) * (99 - (2 * P2)))", + "exp": { + "left": { + "left": 0.0005, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": 99, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + } + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/100 * P2) / (1/100 * P2))", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": "/", + "right": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + } + ], + "guard": { + "comment": "((1/100 * P2) > 0)", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/100 * P2)", + "exp": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "k1", + "type": "real", + "value": 0.001 + }, + { + "name": "k2", + "type": "real", + "value": 0.01 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00034-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "P2", + "op": "≥", + "right": 40 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "P2" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Dimerisation", + "synchronise": [ + "Dimerisation", + "Dimerisation" + ] + }, + { + "result": "Disassociation", + "synchronise": [ + "Disassociation", + "Disassociation" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_P2", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "P2", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props index d7afcd6..1ef42d0 100644 --- a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00034/00034-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 35.728851) ] \ No newline at end of file +P=? [ true U [0,50] (P2 >= 40) ] diff --git a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm index 265a82b..b37f2bc 100644 --- a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // +const double k1 = 0.001; // +const double k2 = 0.01; // // Species P2 module P2 @@ -16,7 +16,7 @@ module P2 P2 : int init 0; // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); + [Dimerisation] P2 >= 0 -> (P2' = P2 + 1); // Disassociation [Disassociation] P2 > 0 -> (P2' = P2 - 1); @@ -28,7 +28,7 @@ module reaction_rates // Dimerisation: -> -> P2 [Dimerisation] (0.5 * k1 * (100 - (2 * P2)) * (99 - (2 * P2))) > 0 -> (0.5 * k1 * (100 - (2 * P2)) * (99 - (2 * P2))) : true; - // Disassociation: -> P2 -> + // Disassociation: -> P2 -> [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.jani new file mode 100644 index 0000000..acf03a3 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.jani @@ -0,0 +1,411 @@ +{ + "actions": [ + { + "name": "Dimerisation" + }, + { + "name": "Disassociation" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 + 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 >= 0)", + "exp": { + "left": "P2", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 - 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 > 0)", + "exp": { + "left": "P2", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_P2 <- P2", + "ref": "rewardmodel_P2", + "value": "P2" + } + ] + } + ], + "name": "P2", + "variables": [] + }, + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2) / (((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2))", + "exp": { + "left": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + } + } + } + } + ], + "guard": { + "comment": "((((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2) > 0)", + "exp": { + "left": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2)", + "exp": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + } + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/100 * P2) / (1/100 * P2))", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": "/", + "right": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + } + ], + "guard": { + "comment": "((1/100 * P2) > 0)", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/100 * P2)", + "exp": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "k1", + "type": "real", + "value": 0.001 + }, + { + "name": "k2", + "type": "real", + "value": 0.01 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00035-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "P2", + "op": "≥", + "right": 36 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "P2" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Dimerisation", + "synchronise": [ + "Dimerisation", + "Dimerisation" + ] + }, + { + "result": "Disassociation", + "synchronise": [ + "Disassociation", + "Disassociation" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_P2", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "P2", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props index 065c787..f37ff17 100644 --- a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00035/00035-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 35.728851) ] \ No newline at end of file +P=? [ true U [0,50] (P2 >= 36) ] diff --git a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm index 85e9280..5952074 100644 --- a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // +const double k1 = 0.001; // +const double k2 = 0.01; // // Species P2 module P2 @@ -16,7 +16,7 @@ module P2 P2 : int init 0; // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); + [Dimerisation] P2 >= 0 -> (P2' = P2 + 1); // Disassociation [Disassociation] P2 > 0 -> (P2' = P2 - 1); @@ -28,7 +28,7 @@ module reaction_rates // Dimerisation: -> -> P2 [Dimerisation] ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) > 0 -> ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) : true; - // Disassociation: -> P2 -> + // Disassociation: -> P2 -> [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.jani new file mode 100644 index 0000000..b6b9972 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.jani @@ -0,0 +1,411 @@ +{ + "actions": [ + { + "name": "Dimerisation" + }, + { + "name": "Disassociation" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 + 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "+", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 >= 0)", + "exp": { + "left": "P2", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "assignments": [ + { + "comment": "P2 <- (P2 - 1)", + "ref": "P2", + "value": { + "left": "P2", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(P2 > 0)", + "exp": { + "left": "P2", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_P2 <- P2", + "ref": "rewardmodel_P2", + "value": "P2" + } + ] + } + ], + "name": "P2", + "variables": [] + }, + { + "edges": [ + { + "action": "Dimerisation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2) / (((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2))", + "exp": { + "left": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + }, + "op": "/", + "right": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + } + } + } + } + ], + "guard": { + "comment": "((((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2) > 0)", + "exp": { + "left": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(((1/1000 * (100 - (2 * P2))) * ((100 - (2 * P2)) - 1)) / 2)", + "exp": { + "left": { + "left": { + "left": 0.001, + "op": "*", + "right": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + } + }, + "op": "*", + "right": { + "left": { + "left": 100, + "op": "-", + "right": { + "left": 2, + "op": "*", + "right": "P2" + } + }, + "op": "-", + "right": 1 + } + }, + "op": "/", + "right": 2 + } + } + }, + { + "action": "Disassociation", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/100 * P2) / (1/100 * P2))", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": "/", + "right": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + } + ], + "guard": { + "comment": "((1/100 * P2) > 0)", + "exp": { + "left": { + "left": 0.01, + "op": "*", + "right": "P2" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/100 * P2)", + "exp": { + "left": 0.01, + "op": "*", + "right": "P2" + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "k1", + "type": "real", + "value": 0.001 + }, + { + "name": "k2", + "type": "real", + "value": 0.01 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00036-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "P2", + "op": "≥", + "right": 40 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "P2" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Dimerisation", + "synchronise": [ + "Dimerisation", + "Dimerisation" + ] + }, + { + "result": "Disassociation", + "synchronise": [ + "Disassociation", + "Disassociation" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_P2", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "P2", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props index bce2685..620fbdd 100644 --- a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00036/00036-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 35.728851) ] \ No newline at end of file +P=? [ true U [0,50] (P2 >= 40) ] diff --git a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm index 614a45c..5661ea1 100644 --- a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double k1 = 0.001; // -const double k2 = 0.01; // +const double k1 = 0.001; // +const double k2 = 0.01; // // Species P2 module P2 @@ -16,7 +16,7 @@ module P2 P2 : int init 0; // Dimerisation - [Dimerisation] P2 > 0 -> (P2' = P2 + 1); + [Dimerisation] P2 >= 0 -> (P2' = P2 + 1); // Disassociation [Disassociation] P2 > 0 -> (P2' = P2 - 1); @@ -28,7 +28,7 @@ module reaction_rates // Dimerisation: -> -> P2 [Dimerisation] ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) > 0 -> ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) : true; - // Disassociation: -> P2 -> + // Disassociation: -> P2 -> [Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.jani new file mode 100644 index 0000000..d857c19 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 5)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 5 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((1/5 * _X) / (1/5 * _X))", + "exp": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.2, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((1/5 * _X) > 0)", + "exp": { + "left": { + "left": 0.2, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(1/5 * _X)", + "exp": { + "left": 0.2, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.2 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00037-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "≥", + "right": 40 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props index d9f2e98..c98c111 100644 --- a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00037/00037-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X > 24.998865) ] \ No newline at end of file +P=? [ true U [0,50] (_X >= 40) ] diff --git a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm index 99aa25b..416d262 100644 --- a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 0.2; // +const double Alpha = 1.0; // +const double Mu = 0.2; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 5); + [Immigration] _X >= 0 -> (_X' = _X + 5); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> _X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.jani new file mode 100644 index 0000000..6485df8 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 10)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((2/5 * _X) / (2/5 * _X))", + "exp": { + "left": { + "left": 0.4, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 0.4, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((2/5 * _X) > 0)", + "exp": { + "left": { + "left": 0.4, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(2/5 * _X)", + "exp": { + "left": 0.4, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 0.4 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00038-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "≥", + "right": 55 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props index 01e79da..3ee1426 100644 --- a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00038/00038-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X = 25.0) ] \ No newline at end of file +P=? [ true U [0,50] (_X >= 55) ] diff --git a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm index d2c93c9..a7b2375 100644 --- a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 0.4; // +const double Alpha = 1.0; // +const double Mu = 0.4; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 10); + [Immigration] _X >= 0 -> (_X' = _X + 10); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -25,11 +25,10 @@ endmodule // Reaction rates module reaction_rates - // Immigration: -> -> -_X + // Immigration: -> [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.jani b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.jani new file mode 100644 index 0000000..604e235 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.jani @@ -0,0 +1,275 @@ +{ + "actions": [ + { + "name": "Death" + }, + { + "name": "Immigration" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X - 1)", + "ref": "_X", + "value": { + "left": "_X", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X > 0)", + "exp": { + "left": "_X", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Immigration", + "destinations": [ + { + "assignments": [ + { + "comment": "_X <- (_X + 100)", + "ref": "_X", + "value": { + "left": "_X", + "op": "+", + "right": 100 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(_X >= 0)", + "exp": { + "left": "_X", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel__X <- _X", + "ref": "rewardmodel__X", + "value": "_X" + } + ] + } + ], + "name": "_X", + "variables": [] + }, + { + "edges": [ + { + "action": "Death", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((4 * _X) / (4 * _X))", + "exp": { + "left": { + "left": 4, + "op": "*", + "right": "_X" + }, + "op": "/", + "right": { + "left": 4, + "op": "*", + "right": "_X" + } + } + } + } + ], + "guard": { + "comment": "((4 * _X) > 0)", + "exp": { + "left": { + "left": 4, + "op": "*", + "right": "_X" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(4 * _X)", + "exp": { + "left": 4, + "op": "*", + "right": "_X" + } + } + }, + { + "action": "Immigration", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(1 > 0)", + "exp": true + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "Alpha", + "type": "real", + "value": 1 + }, + { + "name": "Mu", + "type": "real", + "value": 4 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "00039-sbml-l3v2", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "_X", + "op": "≥", + "right": 300 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "_X" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Death", + "synchronise": [ + "Death", + "Death" + ] + }, + { + "result": "Immigration", + "synchronise": [ + "Immigration", + "Immigration" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_X", + "type": "int" + } + ] +} diff --git a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props index ad714ad..c882c75 100644 --- a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props +++ b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props @@ -2,4 +2,4 @@ // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00039/00039-sbml-l3v2.xml // @GeneticLogicLab -P=? [ true U [0,50] (X = 25.0) ] \ No newline at end of file +P=? [ true U [0,50] (_X >= 300) ] diff --git a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm index 0a17d78..92ba27f 100644 --- a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm +++ b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm @@ -7,8 +7,8 @@ ctmc // Compartment size // Model parameters -const double Alpha = 1.0; // -const double Mu = 4.0; // +const double Alpha = 1.0; // +const double Mu = 4.0; // // Species _X module _X @@ -16,7 +16,7 @@ module _X _X : int init 0; // Immigration - [Immigration] _X > 0 -> (_X' = _X + 100); + [Immigration] _X >= 0 -> (_X' = _X + 100); // Death [Death] _X > 0 -> (_X' = _X - 1); @@ -28,7 +28,7 @@ module reaction_rates // Immigration: -> -> d_X [Immigration] Alpha > 0 -> Alpha : true; - // Death: -> _X -> + // Death: -> _X -> [Death] (Mu * _X) > 0 -> (Mu * _X) : true; endmodule diff --git a/Benchmarks/SBMLstochasticTests/00039/results.txt b/Benchmarks/SBMLstochasticTests/00039/results.txt new file mode 100644 index 0000000..7aeb020 --- /dev/null +++ b/Benchmarks/SBMLstochasticTests/00039/results.txt @@ -0,0 +1,2 @@ +0.06627554753035092 +0.06627554753035092 diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props deleted file mode 100644 index e21e7d4..0000000 --- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00040/00040-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm deleted file mode 100644 index 4ca7a81..0000000 --- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00040/00040-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml deleted file mode 100644 index 026fe07..0000000 --- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props deleted file mode 100644 index e096445..0000000 --- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00041/00041-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm deleted file mode 100644 index 532d383..0000000 --- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00041/00041-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double variance = 1.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml deleted file mode 100644 index 34c9a19..0000000 --- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - - - - 2 - - variance - - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props deleted file mode 100644 index 3f78773..0000000 --- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00042/00042-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm deleted file mode 100644 index 179e9e9..0000000 --- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00042/00042-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml deleted file mode 100644 index 1d1bb7a..0000000 --- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - uniform - 0 - 1 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props deleted file mode 100644 index 0ced6ac..0000000 --- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00043/00043-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm deleted file mode 100644 index 8d5c97c..0000000 --- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00043/00043-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml deleted file mode 100644 index 5d9437b..0000000 --- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props deleted file mode 100644 index e9c3b4e..0000000 --- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00044/00044-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm deleted file mode 100644 index 52148c4..0000000 --- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00044/00044-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml deleted file mode 100644 index 9f69cea..0000000 --- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 0.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props deleted file mode 100644 index 616d684..0000000 --- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00045/00045-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm deleted file mode 100644 index f253547..0000000 --- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00045/00045-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml deleted file mode 100644 index e36080a..0000000 --- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - 1 - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props deleted file mode 100644 index f777707..0000000 --- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00046/00046-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2.2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm deleted file mode 100644 index e0fef91..0000000 --- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00046/00046-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml deleted file mode 100644 index fa70c12..0000000 --- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - 2 - 1.1 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props deleted file mode 100644 index 6f36b72..0000000 --- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00047/00047-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm deleted file mode 100644 index 4380dce..0000000 --- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00047/00047-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml deleted file mode 100644 index be3990e..0000000 --- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - poisson - 1.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props deleted file mode 100644 index 9312370..0000000 --- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00048/00048-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm deleted file mode 100644 index 9bfcb9c..0000000 --- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00048/00048-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml deleted file mode 100644 index bd0828a..0000000 --- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - cauchy - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props deleted file mode 100644 index e92c4f5..0000000 --- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00049/00049-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm deleted file mode 100644 index 14fceb2..0000000 --- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00049/00049-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml deleted file mode 100644 index 501f694..0000000 --- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - cauchy - 1 - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props deleted file mode 100644 index 7a9b1b0..0000000 --- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00050/00050-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm deleted file mode 100644 index 071d6a3..0000000 --- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00050/00050-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml deleted file mode 100644 index 9297b03..0000000 --- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - chisquare - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props deleted file mode 100644 index 8375089..0000000 --- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00051/00051-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 3.2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm deleted file mode 100644 index 573dda1..0000000 --- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00051/00051-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml deleted file mode 100644 index 30bdbcc..0000000 --- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - chisquare - 3.2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props deleted file mode 100644 index 6804b95..0000000 --- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00052/00052-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2.506628275) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm deleted file mode 100644 index 02c6c2c..0000000 --- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00052/00052-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml deleted file mode 100644 index a28e544..0000000 --- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - rayleigh - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props deleted file mode 100644 index adbd938..0000000 --- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00053/00053-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.23) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm deleted file mode 100644 index c9b3944..0000000 --- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00053/00053-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml deleted file mode 100644 index 5910523..0000000 --- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml +++ /dev/null @@ -1,50 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - bernoulli - 0.23 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props deleted file mode 100644 index dd51a91..0000000 --- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00054/00054-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm deleted file mode 100644 index 39230c8..0000000 --- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00054/00054-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml deleted file mode 100644 index a9bb9bf..0000000 --- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - laplace - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props deleted file mode 100644 index e2204ea..0000000 --- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00055/00055-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm deleted file mode 100644 index ab51a22..0000000 --- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00055/00055-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml deleted file mode 100644 index dc5433d..0000000 --- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - laplace - 1 - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props deleted file mode 100644 index 99e1b4b..0000000 --- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00056/00056-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm deleted file mode 100644 index a22c106..0000000 --- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00056/00056-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml deleted file mode 100644 index 83f067c..0000000 --- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - lognormal - 1 - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props deleted file mode 100644 index a28f39e..0000000 --- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00057/00057-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 20) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm deleted file mode 100644 index 5b07837..0000000 --- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00057/00057-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml deleted file mode 100644 index 104fec3..0000000 --- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - binomial - 100 - 0.2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props deleted file mode 100644 index 5de8be8..0000000 --- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00058/00058-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 20.6064) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm deleted file mode 100644 index a102679..0000000 --- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00058/00058-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml deleted file mode 100644 index 4ed6b60..0000000 --- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - binomial - 100 - 0.2 - 15 - 32 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props deleted file mode 100644 index 9801bc0..0000000 --- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00059/00059-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 3.348) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm deleted file mode 100644 index eb9a145..0000000 --- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00059/00059-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml deleted file mode 100644 index 1babf9f..0000000 --- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - cauchy - 1 - 2 - 1.1 - 10 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props deleted file mode 100644 index d001825..0000000 --- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00060/00060-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 3.6835) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm deleted file mode 100644 index a81eacf..0000000 --- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00060/00060-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml deleted file mode 100644 index 2ebfb94..0000000 --- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - chisquare - 2 - 2 - 8 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props deleted file mode 100644 index 7899f8f..0000000 --- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00061/00061-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2.995) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm deleted file mode 100644 index 1f56d31..0000000 --- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00061/00061-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml deleted file mode 100644 index 1080ac2..0000000 --- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - 2 - 9 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props deleted file mode 100644 index 3b9c6bc..0000000 --- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00062/00062-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 4.1382735) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm deleted file mode 100644 index 67eb058..0000000 --- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00062/00062-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml deleted file mode 100644 index e32de8b..0000000 --- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - 1 - 2 - 3 - 6 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props deleted file mode 100644 index fe1b3ec..0000000 --- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00063/00063-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 3.84976) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm deleted file mode 100644 index 5c99646..0000000 --- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00063/00063-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml deleted file mode 100644 index eafdec1..0000000 --- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - laplace - 1 - 2 - 2 - 10 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props deleted file mode 100644 index 122d87f..0000000 --- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00064/00064-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1.68) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm deleted file mode 100644 index a82e277..0000000 --- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00064/00064-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml deleted file mode 100644 index f02d2c3..0000000 --- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - lognormal - 1 - 2 - 3 - 10 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props deleted file mode 100644 index d97629b..0000000 --- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00065/00065-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2.6364) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm deleted file mode 100644 index a00f75e..0000000 --- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00065/00065-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml deleted file mode 100644 index 6b4a0cf..0000000 --- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - poisson - 1.5 - 2 - 18 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props deleted file mode 100644 index fb1973d..0000000 --- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00066/00066-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 3.76665) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm deleted file mode 100644 index 02229f2..0000000 --- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00066/00066-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml deleted file mode 100644 index 0e6631c..0000000 --- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - rayleigh - 2 - 3 - 5 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props deleted file mode 100644 index 04ea464..0000000 --- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00067/00067-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm deleted file mode 100644 index 7aad191..0000000 --- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00067/00067-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double truncationLowerBound = -0.5; // -const double truncationUpperBound = 0.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml deleted file mode 100644 index 87f7a55..0000000 --- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 0.5 - truncationLowerBound - truncationUpperBound - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props deleted file mode 100644 index f26aeb4..0000000 --- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00068/00068-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.479252959) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm deleted file mode 100644 index 7b274af..0000000 --- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm +++ /dev/null @@ -1,31 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00068/00068-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double _rate = 1.0; // -const double truncationLowerBound = 0.25; // -const double truncationUpperBound = 0.75; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml deleted file mode 100644 index 5459788..0000000 --- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - rate - truncationLowerBound - truncationUpperBound - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props deleted file mode 100644 index 008437f..0000000 --- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00069/00069-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.897735417) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm deleted file mode 100644 index 487f36b..0000000 --- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00069/00069-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml deleted file mode 100644 index 22a5f84..0000000 --- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - - - 0.5 - - - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props deleted file mode 100644 index a3566dd..0000000 --- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00070/00070-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = -0.897735417) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm deleted file mode 100644 index 70f217e..0000000 --- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00070/00070-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml deleted file mode 100644 index 907743a..0000000 --- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - - - - - 0.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props deleted file mode 100644 index efca5c1..0000000 --- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00071/00071-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1.532245529) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm deleted file mode 100644 index e170656..0000000 --- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00071/00071-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml deleted file mode 100644 index b64942f..0000000 --- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - 0.5 - - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props deleted file mode 100644 index 24903bf..0000000 --- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00072/00072-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = -1.532245529) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm deleted file mode 100644 index 45e410f..0000000 --- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00072/00072-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml deleted file mode 100644 index 8997450..0000000 --- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml +++ /dev/null @@ -1,61 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - - - - - - - 0.5 - - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props deleted file mode 100644 index cb499bb..0000000 --- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00073/00073-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm deleted file mode 100644 index 26fda6a..0000000 --- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00073/00073-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml deleted file mode 100644 index ac20bb1..0000000 --- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 0.5 - - - 0.5 - - 0.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props deleted file mode 100644 index d23c452..0000000 --- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00074/00074-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm deleted file mode 100644 index 0517600..0000000 --- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00074/00074-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double variance = 0.25; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml deleted file mode 100644 index e1f5315..0000000 --- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - - - - 2 - - variance - - -0.5 - 0.5 - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props deleted file mode 100644 index f948974..0000000 --- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00075/00075-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.178136442) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm deleted file mode 100644 index b039087..0000000 --- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00075/00075-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml deleted file mode 100644 index 933bdc6..0000000 --- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 0.5 - - - 0.25 - - 0.75 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props deleted file mode 100644 index 9d0cf68..0000000 --- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00076/00076-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.460322303) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm deleted file mode 100644 index 6ae2ef5..0000000 --- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00076/00076-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml deleted file mode 100644 index 838b01c..0000000 --- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 0.5 - 0.25 - 0.75 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props deleted file mode 100644 index 7386756..0000000 --- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00077/00077-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1.25) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm deleted file mode 100644 index c3b0e9b..0000000 --- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00077/00077-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml deleted file mode 100644 index 0037b24..0000000 --- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - 0.25 - - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props deleted file mode 100644 index 6c2b095..0000000 --- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00078/00078-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.328558649) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm deleted file mode 100644 index 8b7dfb6..0000000 --- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00078/00078-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml deleted file mode 100644 index 47129d1..0000000 --- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - - - - - 0.75 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props deleted file mode 100644 index 53c6b7c..0000000 --- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00079/00079-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.479252959) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm deleted file mode 100644 index af5c36e..0000000 --- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm +++ /dev/null @@ -1,28 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00079/00079-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml deleted file mode 100644 index ca86743..0000000 --- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - 0.25 - 0.75 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props deleted file mode 100644 index 2d5515d..0000000 --- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00080/00080-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm deleted file mode 100644 index c901357..0000000 --- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00080/00080-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double mean = 0.0; // -const double stddev = 1.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml deleted file mode 100644 index 54d06fe..0000000 --- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - mean - stddev - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props deleted file mode 100644 index b03ae9c..0000000 --- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00081/00081-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm deleted file mode 100644 index 65e87f0..0000000 --- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00081/00081-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double mean = 0.0; // -const double variance = 1.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml deleted file mode 100644 index 5d644e8..0000000 --- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - mean - - - - 2 - - variance - - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props deleted file mode 100644 index 4823e46..0000000 --- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00082/00082-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm deleted file mode 100644 index f6e1f1c..0000000 --- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00082/00082-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double minimum = 0.0; // -const double maximum = 1.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml deleted file mode 100644 index ec40ea6..0000000 --- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - uniform - minimum - maximum - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props deleted file mode 100644 index fb825da..0000000 --- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00083/00083-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm deleted file mode 100644 index c079978..0000000 --- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00083/00083-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double _rate = 1.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml deleted file mode 100644 index 26a03c8..0000000 --- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - rate - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props deleted file mode 100644 index 506c085..0000000 --- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00084/00084-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm deleted file mode 100644 index e257817..0000000 --- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00084/00084-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double _rate = 0.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml deleted file mode 100644 index 327d60f..0000000 --- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - rate - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props deleted file mode 100644 index 1985b09..0000000 --- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00085/00085-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm deleted file mode 100644 index 934faab..0000000 --- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00085/00085-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double shape = 1.0; // -const double scale = 2.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml deleted file mode 100644 index 6477daf..0000000 --- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - shape - scale - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props deleted file mode 100644 index b72ab8a..0000000 --- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00086/00086-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2.2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm deleted file mode 100644 index 2685c99..0000000 --- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00086/00086-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double shape = 2.0; // -const double scale = 1.1; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml deleted file mode 100644 index 0994a92..0000000 --- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - shape - scale - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props deleted file mode 100644 index 22dd2d6..0000000 --- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00087/00087-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 1.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm deleted file mode 100644 index df9efa7..0000000 --- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00087/00087-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double _rate = 1.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml deleted file mode 100644 index a1a5ff7..0000000 --- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - poisson - rate - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props deleted file mode 100644 index d19787e..0000000 --- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00088/00088-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm deleted file mode 100644 index 2961bf2..0000000 --- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00088/00088-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double stddev = 1.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml deleted file mode 100644 index d9b6a87..0000000 --- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - stddev - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props deleted file mode 100644 index 6a0e7cd..0000000 --- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00089/00089-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.479252959) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm deleted file mode 100644 index abba6d1..0000000 --- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00089/00089-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double truncationLowerBound = 0.25; // -const double truncationUpperBound = 0.75; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml deleted file mode 100644 index 323c126..0000000 --- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml +++ /dev/null @@ -1,56 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - exponential - 1 - truncationLowerBound - truncationUpperBound - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props deleted file mode 100644 index b13b64c..0000000 --- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00090/00090-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm deleted file mode 100644 index f47820c..0000000 --- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00090/00090-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double mean = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml deleted file mode 100644 index 535f642..0000000 --- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - mean - 1.5 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props deleted file mode 100644 index 9dd4e33..0000000 --- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00091/00091-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm deleted file mode 100644 index ebad134..0000000 --- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00091/00091-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double mean = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml deleted file mode 100644 index a9739cf..0000000 --- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml +++ /dev/null @@ -1,58 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - mean - - - - 2 - - 1.5 - - - - - - - -0.5 - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props deleted file mode 100644 index ac1160a..0000000 --- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00092/00092-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm deleted file mode 100644 index d0f93a1..0000000 --- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00092/00092-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double maximum = 1.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml deleted file mode 100644 index b0e6c16..0000000 --- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - uniform - 0 - maximum - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props deleted file mode 100644 index 79da70a..0000000 --- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00093/00093-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0.5) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm deleted file mode 100644 index b9212d7..0000000 --- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00093/00093-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double minimum = 0.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml deleted file mode 100644 index 70b0ec1..0000000 --- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - uniform - minimum - 1 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props deleted file mode 100644 index 045183f..0000000 --- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00094/00094-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm deleted file mode 100644 index a9d1fec..0000000 --- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00094/00094-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double scale = 2.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml deleted file mode 100644 index 08d0c47..0000000 --- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - 1 - scale - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props deleted file mode 100644 index 67cca9e..0000000 --- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00095/00095-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 2) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm deleted file mode 100644 index 1007735..0000000 --- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm +++ /dev/null @@ -1,29 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00095/00095-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double shape = 1.0; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml deleted file mode 100644 index 1faa4f9..0000000 --- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml +++ /dev/null @@ -1,54 +0,0 @@ - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - gamma - shape - 2 - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props deleted file mode 100644 index 9adb52b..0000000 --- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00099/00099-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = -0.897735417) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm deleted file mode 100644 index 74a1254..0000000 --- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm +++ /dev/null @@ -1,30 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00099/00099-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double truncationLowerBound = -Infinity; // -const double truncationUpperBound = 0.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml deleted file mode 100644 index 4c74504..0000000 --- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml +++ /dev/null @@ -1,57 +0,0 @@ - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - 0 - 1.5 - truncationLowerBound - truncationUpperBound - - - - - - - - 0.5 - - - - - - - - diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props deleted file mode 100644 index d4b8798..0000000 --- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props +++ /dev/null @@ -1,5 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00100/00100-sbml-l3v2.xml -// @GeneticLogicLab - -P=? [ true U [0,50] (X = 0) ] \ No newline at end of file diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm deleted file mode 100644 index 3d928eb..0000000 --- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm +++ /dev/null @@ -1,32 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00100/00100-sbml-l3v2.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double _C = 1.0; - -// Model parameters -const double t = 0.0; // -const double mean = 0.0; // -const double stddev = 0.5; // -const double truncationLowerBound = -0.5; // -const double truncationUpperBound = 0.5; // - -// Species _X -module _X - - _X : int init 0; - - -endmodule - -// Reaction rates -module reaction_rates - -endmodule - -// Reward structures (one per species) -// Reward 1: _X -rewards "_X" true : _X; endrewards diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml deleted file mode 100644 index 0ad040d..0000000 --- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml +++ /dev/null @@ -1,59 +0,0 @@ - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - t - 0.5 - - - - - - - - normal - mean - stddev - truncationLowerBound - truncationUpperBound - - - - - - - - 0.5 - - - - - - - - diff --git a/ChemicalReactionNetworks/EnzymaticFutileCycle/EnzymaticFutileCycle.jani b/ChemicalReactionNetworks/EnzymaticFutileCycle/EnzymaticFutileCycle.jani new file mode 100644 index 0000000..6f9ee0f --- /dev/null +++ b/ChemicalReactionNetworks/EnzymaticFutileCycle/EnzymaticFutileCycle.jani @@ -0,0 +1,1423 @@ +{ + "actions": [ + { + "name": "R0" + }, + { + "name": "R1" + }, + { + "name": "R2" + }, + { + "name": "R3" + }, + { + "name": "R4" + }, + { + "name": "R5" + } + ], + "automata": [ + { + "edges": [ + { + 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a/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt b/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt new file mode 100644 index 0000000..63fa93f --- /dev/null +++ b/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt @@ -0,0 +1,2 @@ +0.0 +2.0523367282828658E-4 diff --git a/FaultTolerance/README.md b/FaultTolerance/README.md deleted file mode 100644 index db151fc..0000000 --- a/FaultTolerance/README.md +++ /dev/null @@ -1,76 +0,0 @@ -# Fault Tolerance Computing and Electronics - -This directory contains models in the fault tolerance domain. - -At present there are two subdirectories containing -specialized models: - -``` -|-- Redundancy -| |-- RFB -| `-- TMR -`-- StochasticComputing - |-- divide_by_two - `-- divider -``` - -An overview of each subcategory and the specific models is -provided in the text below. All of the provided cases are -designed to model transient noise or "soft" upsets, as opposed -to permanent hardware defects. - - -# Redundancy Models - -Fault tolerant systems usually have redundant modules and/or signals -so that the system's correct function can be recovered, even in the -event of an error. - -## TMR: Triple Modular Redundancy - -This model represents a classic "majority vote" redundancy technique -that has been deployed in critical systems since the 1960s. The TMR -model has a low state complexity and is provided mainly as a benchmark -for judging the RFB model. - -## RFB: Restorative Feedback - -This model is an updated form of TMR designed to suppress transient -faults. RFB is also suitable for fault tolerance with non-binary -discrete signals as might be encountered in a data communication bus -or high-density Flash memory. Due to its feedback dynamics and -non-binary signals, RFB can have a large or infinite state complexity. - -Two PRISM models are provided: - -* `rfb.pm` -- a binary-valued model with low state complexity. -* `rfb_inf.pm` -- a multiple-valued model with infinite state complexity. - - -# Stochastic Computing Models - -Fault tolerant systems sometimes employ "approximate" computing strategies -for masking or detecting errors in arithmetic or signal processing -circuits. Stochastic computing circuits operate by filtering pseudo- -random bit-streams (PRBS) wherein the computation depends on the overall -average value rather than any particular bit. These circuits are therefore -insensitive to a small number of transient upsets. - -## Divide-By-Two Circuit - -The stochastic divide-by-two function is based on the toggle flip-flop, -which provides a uniform output probability (i.e. average) independent -of the input probability. By using a simple feedback arrangement, this -property can be used to divide a PRBS value by 2. - - -## Divider - -The divider circuit uses a counter to estimate a PRBS probability and -"re-emit" an independent PRBS with the same average value. The re- -emitted stream is then used in feedback to obtain the ratio of two -PRBS averages. Two models are provided: - -* `divider.pm` -- a finite-state model with a fixed counter precision. -* `divider_inf.pm` -- an infinite-state model with a variable counter precision. - diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/README.md b/FaultTolerance/Redundancy/RestorativeFeedback/README.md deleted file mode 100644 index 895b310..0000000 --- a/FaultTolerance/Redundancy/RestorativeFeedback/README.md +++ /dev/null @@ -1,242 +0,0 @@ -# Restorative Feedback (RFB) Model - -This case example models a restorative feedback (RFB) circuit -for in-situ transient error correction in logic circuits and -systems. RFB can be classified as a type of Triple Modular -Redundancy (TMR) wherein logic functions and signals are -instantiated in triplicate. Classical TMR systems use majority -vote to correct a single error, but cannot detect or correct -muliple errors. The RFB circuit is designed to correct momentary -upsets with better reliability than Majority TMR. RFB is able -to suppress multiple momentary faults when the feedback is -active. - -There are two RFB models provided: - -* `rfb.pm` -- a PRISM model for a binary-valued RFB circuit with finite state complexity. - Properties are given in `rfb.props`. -* `rfb_inf.pm` -- a PRISM model for a multiple-valued RFB circuit with infinite state complexity. - Properties are given in `rfb_inf.props`. - - -## Description of the Binary RFB Circuit - -The RFB circuit is based on a modified Muller C-element gate. -The classical C-element is a binary-valued latch with behavior -described as - -``` -if (A==B) - C = A; -``` - -When `A!=B` there is no change in `C`. - -In the RFB circuit, the modified C-element has two modes depending -on an external clock. When the clock is low, the C-element is initialized -to the value of an extra input `I`. When the clock is high, the C-element -behaves as usual: - -``` -if (clk) begin - if (A==B) - C = A; -end else - C = I; -``` - -![Modified Celement with initialization input.](../../../Media/ModifiedCElement.png) - -The RFB circuit shown below presumes that a logic system is replicated for a total -of three instances. Three logic signals x0, x1, and x2 represent instances -the same logic value. Any of the signals may momentarily "flip" to an -erroneous value due to interference or noise. When the clock signal (not shown) -is low, the outputs y0, y1, and y2 are initialized to values sampled from -x1, x2, and x0, respectively. When the clock is high, the C-element outputs -are passed in a feedback cycle which corrects errors and suppresses further upsets. - -![RFB circuit.](../../../Media/RFBCircuit.png) - -To see how a single error is corrected, suppose x0 is initially in error, -so the input values are (x0,x1,x2)=(1,0,0). During the initialization, -the output values are set to (y0,y1,y2)=(x3,x1,x2)=(0,1,0). When the -clock swings high, the three C-elements see respective inputs (1,0), -(0,0) and (0,1). Since C2 sees inputs (0,0), its output is changed to -y2=0, so the outputs finally become (0,0,0) and the error is corrected. - -Reference: - -* Chris Winstead, Yi Luo, Eduardo Monzon, and Abiezer Tejeda, - "An Error Correction Method for Binary and Multiple-Valued Logic", - *IEEE International Symposium on Multiple-Valued Logic*, 2011. -* Chris Winstead, Yi Luo, Eduardo Monzon, and Abiezer Tejeda, - "Error Correction via Restorative Feedback in M-ary Logic Circuits", - *J. of Multiple Valued Logic and Soft Computing*, Vol. 23, pp. 337, 2014. - - -### PRISM Model for the Binary RFB Circuit - -The PRISM model for this circuit is provided in -`rfb.pm`. The input signals are assumed to be 0 (when correct), -so a value of `1` indicates an error. The momentary upset rate -is specified via constant `epsilon`, and the signal recovery rate -is `Rc`. There is also a latch upset rate `alpha` which affects -the C-element memory. - -For a C-element with inputs `A` and `B`, upsets are modeled as -follows: - -* When `A=B`: not susceptible to state upsets. -* When `A!=B`: susceptible to upset with rate `alpha`. - -The initial states are constrained by the integer -constant named `initialErrors`, which indicates how -many signal errors occur when the clock transitions from -low to high. The PRISM model represents behavior during -the correction phase, where the speed and ultimate error -probability are determined by the circuit's feedback -dynamics. - -Two example properties are given in `rfb.props`: - -* `P=? [ F[T,T] y1+y2+y3>1 ]` evaluates the probability -that a non-correctable error state exists at time `T`. The -constant `T` is a `double` indicating the elapsed time in -the circuit's correction phase. -* `S=? [ y1+y2+y3>1 ]` evaluates the steady-state probability -that a non-correctable error state exists in the circuit's -output. - - -### Example results: - -The results given here are informative in comparison to the classical -TMR model located in `../TMR`, demonstrating that RFB is more -reliable for a system with the indicated parameters. - - -#### `T=0`, `initialErrors=1` - -This case models the initial error probability before activating -restorative feedback. Since there is initially only one error, -we expect the timed property to be zero. - -``` -prism -const T=0 -const initialErrors=1 rfb.pm rfb.props -``` - -For the first property (at `T=0`) PRISM returns: - -``` -Result: [0.0,0.0] -``` - -For the second property (steady state) PRISM returns: - -``` -Result: [1.272254163993728E-6,1.272254163993728E-6] -``` - -#### `T=1.0`, `initialErrors=1` - -This case models the error probability 1.0 time units after -activating restorative feedback. This case provides -information about the circuit's transient reliability. - -``` -prism -const T=1.0 -const initialErrors=1 rfb.pm rfb.props -``` - -For the first property (at `T=0`) PRISM returns: - -``` -Result: [4.3735439267849973E-4,4.3735439267849984E-4] -``` - -For the second property (steady state) PRISM returns: - -``` -Result: [1.272254163993728E-6,1.272254163993728E-6] -``` - - -## Description of the Multiple-Valued RFB Circuit - -One of the motivations for the RFB method is to apply TMR -to systems with non-binary signals. Classical TMR relies on -Majority logic that requires two of the three signals be -equal. In systems with multiple-valued signals, all three -signals may differ, so there is no majority. In that situation, -the C-element's latching behavior provides a solution. - -The multiple-valued C-Element and RFB circuit have the same -design as the binary case, except that the signals are allowed -to be arbitrary discrete levels. The upset processes are now -also multiple-valued, requiring more complex models. - - -### PRISM Model for the Multiple-Valued RFB Circuit - -The PRISM model for this circuit is provided in -`rfb_inf.pm`. The input signals are assumed to be 0 (when correct). -The momentary upset rate is specified via constant `epsilon`, and -the signal recovery rate is `Rc`. Since the signal values are non-binary, -the upset amplitude is modeled by a "noise" signal with rate `Rn`. -The noise amplitude distribution is: - -* n=1 with rate `Rn` -* n=2 with rate `Rn/2` -* n=3 with rate `Rn/4` -* n=4 with rate `Rn/8` - -This example noise process is not based on any specific physical model, -but is similar to "random telegraph noise" known to affect various FET -and memristor devices. - -There is also a latch upset rate `alpha` which affects the C-element memory. -Here the latch upset is identical to the binary-valued circuit. Latch upsets -always have amplitude 1, i.e. the C-element output drifts to an adjacent -signal level. - -Initial values for this model are given explicitly via integer constants -`i1`, `i2`, and `i3`, so a single initial state is specified (the binary- -valued circuit allowed specifying an ensemble of initial states, but that -is not possible here). - -Property definitions are more challenging for the multiple-valued circuit -compared to the binary case. Steady-state properties are not available -due to the model's unbounded state complexity. One property is provided -in `rfb_inf.props`: - -* `P=? [ F[T,T] y1+y2+y3!=0 ]` - -This evaluates the probability that the output signals are error-free at -time `T`. - -### Example Results for the Multiple-Valued Circuit - -#### `i1=0`, `i2=3`, `i3=1`, `T=20` - -``` -prism -sim -const i1=0 -const i2=3 -const i3=1 -const T=20 rfb_inf.pm rfb_inf.props -``` - -The result reported by PRISM is - -``` -Result: 0.051 (+/- 0.017928853962181267 with probability 0.99; rel err 0.3515461561212013) -``` - - -#### `i1=0`, `i2=0`, `i3=1`, `T=20` - -``` -prism -sim -const i1=0 -const i2=0 -const i3=1 -const T=20 rfb_inf.pm rfb_inf.props -``` - -The result reported by PRISM is - -``` -Result: 0.024 (+/- 0.012472826037899055 with probability 0.99; rel err 0.5197010849124606) -``` - diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm deleted file mode 100644 index a421d29..0000000 --- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm +++ /dev/null @@ -1,49 +0,0 @@ -// rfb.pm -// Restorative Feedback model -// A type of Triple Modular Redundancy (TMR) -ctmc - -const double Rc = 10; // signal transition rate of logic gates -const double Rn = 2; // noise process rate -const double epsilon = 1; // transient upset rate -const double alpha = .1; // state upset rate -const double T; -const int i1; -const int i2; -const int i3; - - -// Noise sources -module noise1 - n1: int init 0; - - [] (true) -> Rn:(n1'=1)+(Rn/2):(n1'=2)+(Rn/4):(n1'=3)+(Rn/8):(n1'=4); -endmodule -module noise2 = noise1 [ n1=n2 ] endmodule -module noise3 = noise1 [ n1=n3 ] endmodule - - -// Signal Source -module source1 - x1 : int init i1; - - [] (x1 > 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1) + Rc:(x1'=x1-1); - [] (x1 = 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1); - [] (x1 < 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1) + Rc:(x1'=x1+1); -endmodule - -module source2 = source1 [ x1=x2, i1=i2, n1=n2 ] endmodule -module source3 = source1 [ x1=x3, i1=i3, n1=n3 ] endmodule - - -// Modified Muller C-element -module Cem1 - y1 : int init i3; - - [] (x1 = y3) -> (Rc):(y1' = y3); - [] (x1 != y3) -> (alpha/2):(y1'=y1+1)+(alpha/2):(y1'=y1-1); -endmodule - -module Cem2 = Cem1 [ x1=x2, y1=y2, y3=y1, i3 = i1 ] endmodule -module Cem3 = Cem1 [ x1=x3, y1=y3, y3=y2, i3 = i2 ] endmodule - diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props deleted file mode 100644 index 7228516..0000000 --- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props +++ /dev/null @@ -1 +0,0 @@ -P=? [ F[T,T] y1+y2+y3!=0 ] diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm deleted file mode 100644 index 34858c1..0000000 --- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm +++ /dev/null @@ -1,35 +0,0 @@ -// rfb.pm -// Restorative Feedback model -// A type of Triple Modular Redundancy (TMR) -ctmc - -const double Rc =100; // signal transition rate of logic gates -const double epsilon =1; // transient upset rate -const double alpha =0.01; // state upset rate -const double T; -const int initialErrors; - -// Signal Source -module source1 - x1 : [0..1]; - - [] (true) -> epsilon:(x1'=1) + Rc:(x1'=0); -endmodule - -module source2 = source1 [x1=x2] endmodule -module source3 = source1 [x1=x3] endmodule - - -// Modified Muller C-element -module Cem1 - y1 : [0..1]; - - [] (x1 = y3) -> (Rc):(y1' = y3); - [] (x1 != y3) -> (alpha):(y1'=1-y1); -endmodule - -module Cem2 = Cem1 [y1=y2, x1=x2, y3=y1] endmodule -module Cem3 = Cem1 [y1=y3, x1=x3, y3=y2] endmodule - - -init ((x1+x2+x3=initialErrors) & ((y1=x3)&(y2=x1)&(y3=x2))) endinit diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props deleted file mode 100644 index c72acba..0000000 --- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props +++ /dev/null @@ -1,2 +0,0 @@ -P=? [ F[T,T] y1+y2+y3>1 ] -S=? [ y1+y2+y3>1 ] \ No newline at end of file diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/README.md b/FaultTolerance/Redundancy/TripleModularRedundancy/README.md deleted file mode 100644 index 4184f47..0000000 --- a/FaultTolerance/Redundancy/TripleModularRedundancy/README.md +++ /dev/null @@ -1,100 +0,0 @@ -# Triple Modular Redundancy (TMR) Model - -This case example models a Triple Modular Redundancy (TMR) circuit -wherein logic functions and signals are instantiated in triplicate. -Logic states are corrected using majority vote modules, so that a -single error can be corrected. In this model we assume that all signals -are susceptible to momentary upsets, including the majority outputs. - - -## Description of the Circuit - - -The TMR circuit shown below presumes that a logic system is replicated for a total -of three instances. Three logic signals x0, x1, and x2 represent instances -the same logic value. Any of the signals may momentarily "flip" to an -erroneous value due to interference or noise. The majority gates labeled `M` -output the majority decision among the three input signals. Since the majority -gates may also be susceptible to upsets, there are three independent majority -gates so that there is never a single point of failure. - -![Majority TMR circuit.](../../../Media/MajorityTMR.png) - -Reference: - -* R. E. Lyons and W. Vanderkulk, "The use of triple-modular redundancy to improve -computer reliability." *IBM Journal of Research and Development*, 6(2):200, 1962. - -## PRISM Model - -The PRISM model for this circuit is provided in -`tmr.pm`. The input signals are assumed to be 0 (when correct), -so a value of `1` indicates an error. The momentary upset rate -is specified via constant `epsilon`, and the signal recovery rate -is `Rc`. - -The initial states are constrained by the integer -constant named `initialErrors`, which indicates how -many signal errors are present in the initial state. - -Two example properties are given in `tmr.props`: - -* `P=? [ F[T,T] y1+y2+y3>1 ]` evaluates the probability -that a non-correctable error state exists at time `T`. The -constant `T` is a `double` indicating the elapsed time. -* `S=? [ y1+y2+y3>1 ]` evaluates the steady-state probability -that a non-correctable error state exists in the circuit's -output. - -The TMR's output error probability is not strongly dependent on -time, so these two properties should usually be close to each other. - - -## Example results: - - -### `T=0`, `initialErrors=1` - -This case models the initial error probability. Since the majority -gates have undefined (or unconstrained) initial output values, -the instantaneous error probability is indeteminate. - -``` -prism -const T=0 -const initialErrors=1 tmr.pm tmr.props -``` - -For the first property (at `T=0`) PRISM returns: - -``` -Result: [0.0,1.0] -``` - -For the second property (steady state) PRISM returns: - -``` -Result: [4.94427886688858E-4,4.94427886688858E-4] -``` - -### `T=1.0`, `initialErrors=1` - -This case models the error probability after 1.0 time units. -Since this is well beyond the mean signal recovery time `1/Rc`, -the transient error probability should be nearly equal to the steady -state. - -``` -prism -const T=1.0 -const initialErrors=1 tmr.pm tmr.props -``` - -For the first property (at `T=0`) PRISM returns: - -``` -Result: [4.944279220969286E-4,4.94427973657968E-4] -``` - -For the second property (steady state) PRISM returns: - -``` -Result: [4.94427886688858E-4,4.94427886688858E-4] -``` - diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm b/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm deleted file mode 100644 index 69b9e8e..0000000 --- a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm +++ /dev/null @@ -1,35 +0,0 @@ -// tmr.pm -// Triple Modular Reduncancy model -// using majority logic -ctmc - -const double Rc=100; // signal transition rate of logic gates -const double epsilon=1; // transient upset rate -const double T; -const int initialErrors; - -// Signal Source -module source1 - x1 : [0..1]; - - [] (true) -> epsilon:(x1'=1) + Rc:(x1'=0); -endmodule - -module source2 = source1 [x1=x2] endmodule -module source3 = source1 [x1=x3] endmodule - - -// Majority Gates -module Maj1 - y1 : [0..1]; - - [] (x1 + x2 + x3 > 1) -> (Rc):(y1' = 1) + epsilon:(y1'=0); - [] (x1 + x2 + x3 < 2) -> (Rc):(y1' = 0) + epsilon:(y1'=1); - -endmodule - -module Maj2 = Maj1 [y1=y2] endmodule -module Maj3 = Maj1 [y1=y3] endmodule - - -init (x1+x2+x3=initialErrors) endinit diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props b/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props deleted file mode 100644 index c72acba..0000000 --- a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props +++ /dev/null @@ -1,2 +0,0 @@ -P=? [ F[T,T] y1+y2+y3>1 ] -S=? [ y1+y2+y3>1 ] \ No newline at end of file diff --git a/FaultTolerance/StochasticComputing/divide_by_two/README.md b/FaultTolerance/StochasticComputing/divide_by_two/README.md deleted file mode 100644 index 0107305..0000000 --- a/FaultTolerance/StochasticComputing/divide_by_two/README.md +++ /dev/null @@ -1,76 +0,0 @@ -# Unipolar Stochastic Divide-By-Two Model - -This case example models a stochastic divide-by-two circuit -using the unipolar stochastic numerical format. In the -unipolar format, a signal $x$ is a real number between -0 and 1, encoded probabilistically in a binary signal -$X(t)$. At any time $t$, the signal $X(t)=1$ with -probability $x$, and $X(t)=0$ with probability $1-x$. - -## Description of the Circuit - -The divide-by-two circuit schematic is shown below. It accepts -one stochastic input, $A(t)$, and produces a single output $Q(t)$. -Ideally $Q$ should arrive at a steady-state probability $q=a/2$. - -![Unary divide-by-two schematic](../../../Media/StochasticDivideByTwo.png) - -The principle of operation is as follows. The toggle flip-flop -emits a bitstream $B(t)$ with steady-state probability $b=1/2$, -independent of the input stream probability. The AND gate acts as -a probability multiplier, so it emits a bitstream with probability -$q=ab=q/2$. - -Reference: - -* C. Winstead, "Tutorial on Stochastic Computation," - Chapter 2 in *Stochastic Computing: Techniques and Applications*, - ed. Gaudet and Gross, Springer, 2019. - - -## PRISM Model - -The PRISM model for this circuit is provided in -`divide_by_two.pm`. The input probability is given -via the constant `a`. Internally, the stochastic -input signal is `inA`, and the output signal is `Q`. - -Three example properties are given in `divide_by_two.props`: - -* `P=? [ F[T,T] Q = 1 ]` evaluates the probability -that Q=1 (i.e. the numerical output $q$) at `T` clock cycles, -which relates to the circuit's response time. The constant `T` -is an integer. -* `S=? [ Q = 1 ]` evaluates the steady-state probability -that Q=1. -* `P=? [ F[T,T] Q = 1 ] - S=? [ Q = 1 ]` evaluates the transient -absolute error in output probability at clock cycle `T`. - -## Example results: - -### `a=0.1` and `T=100` - -The expected output is $q=0.05$. - -``` -prism --const a=0.1 --const T=100 divide_by_two.pm divide_by_two.props -``` - -For the first property (at 100 clock cycles) PRISM returns: - -``` -Result: 0.049999999984085816 (exact floating point) -``` - -For the second property (steady state) PRISM returns: - -``` -Result: 0.04999998765587841 -``` - -For the third property (transient error) PRISM returns: - -``` -Result: 1.2328207406320235E-8 -``` - diff --git a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm b/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm deleted file mode 100644 index 03164a2..0000000 --- a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm +++ /dev/null @@ -1,39 +0,0 @@ -// divide_by_two.pm -// Unipolar Stochastic Divide-By-2 -// Based on Toggle Flip-Flop - -dtmc - -const double a; // input value between 0 and 1 -const int T; // clock cycle count - -//------------------ -// Signal Sources -//------------------ -module Source0 - inA : [0..1] init 0; - - [event] (true) -> a:(inA'=1) + (1-a):(inA'=0); -endmodule - -//------------------------ -// Toggle Flip-Flop (TFF) -//------------------------ -module TFF - B : [0..1] init 0; - - [event] (inA=0) -> (B' = B); - [event] (inA=1) -> (B' = 1-B); -endmodule - - -//------------------ -// AND gate -//------------------ -module AND0 - - Q : [0..1] init 0; - - [event] (inA=1 & B=1) -> (Q'=1); - [event] (inA=0 | B=0) -> (Q'=0); -endmodule diff --git a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props b/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props deleted file mode 100644 index cf2de91..0000000 --- a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props +++ /dev/null @@ -1,5 +0,0 @@ -P=? [ F[T,T] Q=1 ] - -S=? [ Q=1 ] - -(P=? [ F[T,T] Q=1 ]) - (S=? [ Q=1 ]) diff --git a/FaultTolerance/StochasticComputing/divider/README.md b/FaultTolerance/StochasticComputing/divider/README.md deleted file mode 100644 index 5fd2591..0000000 --- a/FaultTolerance/StochasticComputing/divider/README.md +++ /dev/null @@ -1,126 +0,0 @@ -# Unipolar Stochastic Divider Model - -This case example models a stochastic divider using -the unipolar stochastic numerical format. In the -unipolar format, a signal $x$ is a real number between -0 and 1, encoded probabilistically in a binary signal -$X(t)$. At any time $t$, the signal $X(t)=1$ with -probability $x$, and $X(t)=0$ with probability $1-x$. - -Two models are provided: - -* `divider.pm` is a finite-state model. -* `divider_inf.pm` is an intinite-state model. - -Both models rely on a finite up-down counter to -estimate the average probability of a unary stochastic -bitstream. The finite counter saturates at `MAX_COUNT`, -which is a fixed constant in the model. - -In the infinite-state model, the counter's limit is -variable, initially +/-1 and increasing logarithmically -with respect to the elapsed clock cycles. This approach -improves accuracy for calculations with small probabilities, -e.g. below 0.01, however the state complexity becomes -unbounded in this model. - - -## Description of the Circuit - -The divider circuit shematic is shown below. It accepts -two stochastic inputs, $A(t)$ and $B(t)$, and produces a -single output $Q(t)$. Ideally $Q$ should arrive at a -steady-state probability $Q(t)=q=a/b$. - -![Unary divider schematic](../../../Media/StochasticUnaryDivider.png) - -The principle of operation is as follows. The signed up/down -counter (UDC) reaches equilibrium when its inputs have equal -probability. The module R emits a bit stream with probability -equal to the counter value C, scaled to the range (0,1). -The AND gate acts as a probability multiplier, so it emits bits -with probability $qb$. Due to the feedback connection, at -steady state we expect $qb=a$ and therefore $q=a/b$. - -Reference: - -* C. Winstead, "Tutorial on Stochastic Computation," - Chapter 2 in *Stochastic Computing: Techniques and Applications*, - ed. Gaudet and Gross, Springer, 2019. - - -## PRISM Model - -The input probabilities are given via constants `a` and `b`. Internally, -the stochastic input signals are `inA` and `inB`, and the output -signal is `Q`. - -Two example properties are given in `divider.props`: - -* `P=? [ F[T,T] Q = 1 ]` evaluates the probability -that Q=1 (i.e. the numerical output $q$) at `T` clock cycles, -which relates to the circuit's response time. The constant `T` -is an integer. -* `S=? [ Q = 1 ]` evaluates the steady-state probability -that Q=1. - -## Example results (finite state model): - -### `a=0.1`, `b=0.3`, and `T=100` - -The expected output is $q=1/3$. - -``` -prism --const a=0.1 --const b=0.3 --const T=100 divider.pm divider.props -``` - -For the first property (at 100 clock cycles) PRISM returns: - -``` -Result: 0.4665562152140168 (exact floating point) -``` - -For the second property (steady state) PRISM returns: - -``` -Result: 0.33333443639168 -``` - - -### `a=0.7`, `b=0.3`, and `T=100` - -In this case the ratio $a/b$ is greather than one, so the expected output -is saturated close to $q=1$. - -``` -prism --const a=0.1 --const b=0.3 --const T=100 divider.pm divider.props -``` - -For the first property (at 100 clock cycles) PRISM returns: - -``` -Result: 0.8790749994268042 (exact floating point) -``` - -For the second property (steady state) PRISM returns: - -``` -Result: 0.9881554646304057 -``` - - -## Example results (infinite state model): - -### `a=0.001`, `b=0.1` - -In this case PRISM is best used to simulate a path with -10,000 clock cycles. The output bitstream `Q` is reported in -column 9 of the output trace. - -``` -prism -simpath time=10000 data -const a=0.001 -const b=0.1 -const T=1000 divider_inf.pm -``` - -In this model PRISM is unable to provide the requested path length, -so it is not possible to compute the long-term transient behavior -or the steady-state output probability using PRISM. diff --git a/FaultTolerance/StochasticComputing/divider/divider.pm b/FaultTolerance/StochasticComputing/divider/divider.pm deleted file mode 100644 index fde5be1..0000000 --- a/FaultTolerance/StochasticComputing/divider/divider.pm +++ /dev/null @@ -1,49 +0,0 @@ -// Unipolar stochastic divider circuit -dtmc - -const double a; -const double b; -const int T; - -// Saturation level for up-down counter -const int MAXCOUNT=63; - -//------------------ -// Signal Sources -//------------------ -module Source0 - inA : [0..1] init 0; - - [event] (inA=0 | inA=1) -> a:(inA'=1) + (1-a):(inA'=0); -endmodule - -// Second signal source: -module Source1 = Source0 [ inA=inB, a=b ] endmodule - - -// AND gate -module AND0 - QB : [0..1] init 0; - - [event] (inB=1)&(Q=1) -> (QB' = 1); - [event] !(inB=1 & Q=1) -> (QB' = 0); -endmodule - - -// Up-Down Counter -module UDC0 - c0: [-MAXCOUNT..MAXCOUNT] init 0; - - [event] (c0 > -MAXCOUNT) & (c0 < MAXCOUNT) -> 1:(c0' = c0 + inA - QB); - [event] (c0 = -MAXCOUNT) -> 1:(c0' = c0 + inA); - [event] (c0 = MAXCOUNT) -> 1:(c0' = c0 - QB); -endmodule - -// Output and Feedback -formula q=(c0+MAXCOUNT+1)/(2*(MAXCOUNT+1)); -module FB0 - Q: [0..1] init 0; - - [event] (c0 >= -MAXCOUNT) & (c0 <= MAXCOUNT) -> q:(Q' = 1) + (1-q):(Q'=0); -endmodule - diff --git a/FaultTolerance/StochasticComputing/divider/divider.props b/FaultTolerance/StochasticComputing/divider/divider.props deleted file mode 100644 index 7ab1358..0000000 --- a/FaultTolerance/StochasticComputing/divider/divider.props +++ /dev/null @@ -1,4 +0,0 @@ -P=? [ F[T,T] Q = 1 ] - -S=? [ Q = 1 ] - diff --git a/FaultTolerance/StochasticComputing/divider/divider_inf.pm b/FaultTolerance/StochasticComputing/divider/divider_inf.pm deleted file mode 100644 index 40b24bd..0000000 --- a/FaultTolerance/StochasticComputing/divider/divider_inf.pm +++ /dev/null @@ -1,54 +0,0 @@ -// Unipolar stochastic divider circuit -dtmc - -const double a; -const double b; -const int T; - -//------------------ -// Signal Sources -//------------------ -module Source0 - inA : [0..1] init 0; - - [event] (inA=0 | inA=1) -> a:(inA'=1) + (1-a):(inA'=0); -endmodule - -// Second signal source: -module Source1 = Source0 [ inA=inB, a=b ] endmodule - - -// AND gate -module AND0 - QB : [0..1] init 0; - - [event] (inB=1)&(Q=1) -> (QB' = 1); - [event] !(inB=1 & Q=1) -> (QB' = 0); -endmodule - - -// Up-Down Counter -module UDC0 - c0: int init 0; - - [event] (true) -> 1:(c0' = c0 + inA - QB); -endmodule - -// Clock Timer -module clockTimer - N: int init 1; - M: int init 1; - - [event] (true) -> 1:(N'=N+1)&(M'=1+round(log(N,2))); -endmodule - - -// Output and Feedback -formula q=(c0+M+1)/(2*(M+1)); -module FB0 - Q: [0..1] init 0; - - [event] (c0 >= -M) & (c0 <= M) -> q:(Q' = 1) + (1-q):(Q'=0); - -endmodule - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl index a87d3b7..46cde8a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl @@ -1,3 +1,3 @@ // Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules -P=? [ true U[0,1000] (YFP_protein < 30) ] +P=? [ true U[0,1000] (YFP_protein <= 30) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml index a4429d7..27aed86 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011_bound.jani new file mode 100644 index 0000000..3339eea --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": 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"type": "int", + "value": 100 + }, + { + "name": "HlyIIR_protein_MAX", + "type": "int", + "value": 100 + }, + { + "name": "PhlF_protein_MAX", + "type": "int", + "value": 100 + }, + { + "name": "YFP_protein_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_AmtRpart_module_sub__pBAD_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_AmtRpart_module_sub__pHlyIIR_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_YFPpart_module_sub__pPhlF_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_YFPpart_module_sub__pBetI_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_BetIpart_module_sub__pHlyIIR_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_BetIpart_module_sub__pTet_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_PhlFpart_module_sub__pTac_MAX", + "type": "int", + "value": 100 + }, + { + "name": "topModel_PhlFpart_module_sub__pAmtR_MAX", + "type": "int", + "value": 100 + }, 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"topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pBAD" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + null, + null, + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "PhlF_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 70, + "name": "YFP_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml index a4429d7..27aed86 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10_bound.jani new file mode 100644 index 0000000..22ff30e --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (100 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (100 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + 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"topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pBAD" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + null, + null, + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "PhlF_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 70, + "name": "YFP_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl index a87d3b7..46cde8a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl @@ -1,3 +1,3 @@ // Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules -P=? [ true U[0,1000] (YFP_protein < 30) ] +P=? 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"rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": 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"PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- 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"transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml index 8ec5919..a55b6e2 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.jani new file mode 100644 index 0000000..a411515 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.jani @@ -0,0 +1,3859 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": "AmtR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": "AmtR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- 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"topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pBAD" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml index 8ec5919..a55b6e2 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_010to100_G0_10_10_RBA_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_010to100_G0_10_10_RBA_bound.jani new file mode 100644 index 0000000..7fafd63 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_010to100_G0_10_10_RBA_bound.jani @@ -0,0 +1,3104 @@ +{ + "actions": [ + { + "name": "Degradation_AmtR_protein" + }, + { + "name": "Degradation_BetI_protein" + }, + { + "name": "Degradation_HlyIIR_protein" + }, + { + "name": "Degradation_PhlF_protein" + }, + { + "name": "Degradation_YFP_protein" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein <= (1000 - 10))", + "exp": { + "left": "YFP_protein", + "op": "≤", + "right": 990 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein <= (1000 - 10))", + "exp": { + "left": "YFP_protein", + "op": "≤", + "right": 990 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (1000 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 990 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"PhlF_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein > 9)", + "exp": { + "left": "PhlF_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein <= (1000 - 10))", + "exp": { + "left": "PhlF_protein", + "op": "≤", + "right": 990 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein <= (1000 - 10))", + "exp": { + "left": "PhlF_protein", + "op": "≤", + "right": 990 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "PhlF_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_HlyIIR_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": 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+ "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (1000 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 990 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_AmtR_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } 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"type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml index 759239c..e420e64 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml @@ -1,785 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -787,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -819,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -850,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -881,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -912,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -943,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1013,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1043,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1084,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1139,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1152,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1181,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1236,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1249,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1278,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1333,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1346,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1375,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1430,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1443,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1472,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1527,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1540,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1569,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1624,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1637,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1666,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1721,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1734,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1763,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1833,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1863,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1904,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1959,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1972,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2001,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml index 759239c..e420e64 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml @@ -1,785 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -787,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -819,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -850,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -881,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -912,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -943,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1013,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1043,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1084,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1139,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1152,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1181,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1236,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1249,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1278,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1333,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1346,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1375,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1430,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1443,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1472,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1527,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1540,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1569,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1624,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1637,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1666,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1721,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1734,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1763,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1833,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1863,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1904,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1959,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1972,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2001,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10_bound.jani new file mode 100644 index 0000000..71b8eac --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (100 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 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+ }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": 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"rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": 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"PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml index fc292cb..2b5878a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.jani new file mode 100644 index 0000000..91c93a2 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.jani @@ -0,0 +1,3859 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + 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+ "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml index fc292cb..2b5878a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_100to010_G0_10_10_RBA.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_100to010_G0_10_10_RBA.jani new file mode 100644 index 0000000..c287ae4 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_100to010_G0_10_10_RBA.jani @@ -0,0 +1,2949 @@ +{ + "actions": [ + { + "name": "Degradation_AmtR_protein" + }, + { + "name": "Degradation_BetI_protein" + }, + { + "name": "Degradation_HlyIIR_protein" + }, + { + "name": "Degradation_PhlF_protein" + }, + { + "name": "Degradation_YFP_protein" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } 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null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + ] + }, + { + "result": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "synchronise": [ + "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + ] + }, + { + "result": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "synchronise": [ + "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_AmtR_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_AmtR_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_PhIF_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_PhIF_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_BetI_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_BetI_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_YFP_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_YFP_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_HIyIIR_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_HIyIIR_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml index 0738ba8..4681d31 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111_bound.jani new file mode 100644 index 0000000..9d8591e --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (100 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (100 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (100 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (100 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + 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"topModel_HlyIIRpart_module_sub__kb", + "type": "real", + "value": 0.0001 + }, + { + "name": "topModel_HlyIIRpart_module_sub__ng", + "type": "real", + "value": 2 + }, + { + "name": "topModel_HlyIIRpart_module_sub__np", + "type": "real", + "value": 10 + }, + { + "name": "topModel_HlyIIRpart_module_sub__ka", + "type": "real", + "value": 0.25 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "Circuit0x8E_100to111_G0_10_10", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "YFP_protein", + "op": "≥", + "right": 10 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 1000, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "AmtR_protein" + }, + { + "automaton": "Ara_AraC_protein" + }, + { + "automaton": "TetR_protein" + }, + { + "automaton": "LacI_protein" + }, + { + "automaton": "BetI_protein" + }, + { + "automaton": "HlyIIR_protein" + }, + { + "automaton": "PhlF_protein" + }, + { + "automaton": "YFP_protein" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "automaton": "topModel_HlyIIRpart_module_sub__pBAD" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml index 0738ba8..4681d31 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_100to111_G0_10_10_RBA.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_100to111_G0_10_10_RBA.jani new file mode 100644 index 0000000..644ba2e --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_100to111_G0_10_10_RBA.jani @@ -0,0 +1,2949 @@ +{ + "actions": [ + { + "name": "Degradation_AmtR_protein" + }, + { + "name": "Degradation_BetI_protein" + }, + { + "name": "Degradation_HlyIIR_protein" + }, + { + "name": "Degradation_PhlF_protein" + }, + { + "name": "Degradation_YFP_protein" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_PhlF_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein - 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein > 9)", + "exp": { + "left": "PhlF_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein >= 0)", + "exp": { + "left": "PhlF_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein >= 0)", + "exp": { + "left": "PhlF_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "PhlF_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_HlyIIR_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 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b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_101to011_G1_10_10.jani new file mode 100644 index 0000000..968e66d --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_101to011_G1_10_10.jani @@ -0,0 +1,3859 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": "AmtR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": "AmtR_protein", + "op": 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null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + 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"name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_101to011_G1_10_10_RBA.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_101to011_G1_10_10_RBA.jani new file mode 100644 index 0000000..ece1187 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_101to011_G1_10_10_RBA.jani @@ -0,0 +1,2949 @@ +{ + "actions": [ + { + "name": "Degradation_AmtR_protein" + }, + { + "name": "Degradation_BetI_protein" + }, + { + "name": "Degradation_HlyIIR_protein" + }, + { + "name": "Degradation_PhlF_protein" + }, + { + "name": "Degradation_YFP_protein" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + 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"ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": 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"topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + ] + }, + { + "result": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 250, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 310, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml index 0b82b26..c9deab8 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.jani new file mode 100644 index 0000000..d227d9e --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.jani @@ -0,0 +1,3859 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + 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"topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml index 0b82b26..c9deab8 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_111to010_G0_10_10_RBA.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_111to010_G0_10_10_RBA.jani new file mode 100644 index 0000000..33b5c31 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_111to010_G0_10_10_RBA.jani @@ -0,0 +1,2949 @@ +{ + "actions": [ + { + "name": "Degradation_AmtR_protein" + }, + { + "name": "Degradation_BetI_protein" + }, + { + "name": "Degradation_HlyIIR_protein" + }, + { + "name": "Degradation_PhlF_protein" + }, + { + "name": "Degradation_YFP_protein" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "name": "R_abstracted_production_Circuit10_10_BetI_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pBAD" + }, + { + "name": "R_abstracted_production_Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "name": "R_abstracted_production_Circuit10_10_PhIF_module_sub__pTac" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI" + }, + { + "name": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_YFP_protein", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein > 9)", + "exp": { + "left": "YFP_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pBetI", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "R_abstracted_production_Circuit10_10_YFP_module_sub__pPhlF", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein + 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(YFP_protein >= 0)", + "exp": { + "left": "YFP_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD <- Circuit10_10_AmtR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pBAD", + "value": "Circuit10_10_AmtR_module_sub__pBAD" + }, + { + "comment": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR <- Circuit10_10_AmtR_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_AmtR_module_sub__pHlyIIR", + "value": "Circuit10_10_AmtR_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR <- Circuit10_10_PhIF_module_sub__pAmtR", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pAmtR", + "value": "Circuit10_10_PhIF_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac <- Circuit10_10_PhIF_module_sub__pTac", + "ref": "rewardmodel_Circuit10_10_PhIF_module_sub__pTac", + "value": "Circuit10_10_PhIF_module_sub__pTac" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR <- Circuit10_10_BetI_module_sub__pHlyIIR", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pHlyIIR", + "value": "Circuit10_10_BetI_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_Circuit10_10_BetI_module_sub__pTet <- Circuit10_10_BetI_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_BetI_module_sub__pTet", + "value": "Circuit10_10_BetI_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI <- Circuit10_10_YFP_module_sub__pBetI", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pBetI", + "value": "Circuit10_10_YFP_module_sub__pBetI" + }, + { + "comment": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF <- Circuit10_10_YFP_module_sub__pPhlF", + "ref": "rewardmodel_Circuit10_10_YFP_module_sub__pPhlF", + "value": "Circuit10_10_YFP_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet <- Circuit10_10_HIyIIR_module_sub__pTet", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pTet", + "value": "Circuit10_10_HIyIIR_module_sub__pTet" + }, + { + "comment": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD <- Circuit10_10_HIyIIR_module_sub__pBAD", + "ref": "rewardmodel_Circuit10_10_HIyIIR_module_sub__pBAD", + "value": "Circuit10_10_HIyIIR_module_sub__pBAD" + } + ] + } + ], + "name": "YFP_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_BetI_protein", + 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"int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_YFP_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_HIyIIR_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "Circuit10_10_HIyIIR_module_sub__pBAD", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml index 3d7a277..23704cd 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100_bound.jani new file mode 100644 index 0000000..c0d2a9d --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (310 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (310 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (310 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (310 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + 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"topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + }, + { + "initial-value": 2, + "name": "topModel_HlyIIRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 310 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml index 3d7a277..23704cd 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml @@ -1,786 +1,535 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -788,31 +537,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -820,30 +579,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -851,30 +620,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +661,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +702,40 @@ BetI_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,52 +743,76 @@ AmtR_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1014,18 +837,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1044,30 +864,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1085,52 +899,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1140,11 +978,8 @@ - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pHlyIIR + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1153,18 +988,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1182,52 +1014,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1237,11 +1093,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1250,18 +1103,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1279,52 +1129,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1334,11 +1208,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1347,18 +1218,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1376,52 +1244,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1431,11 +1323,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1444,18 +1333,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1473,52 +1359,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1528,11 +1438,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1541,18 +1448,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1570,52 +1474,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1625,11 +1553,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1638,18 +1563,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1667,52 +1589,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1722,11 +1668,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1735,18 +1678,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1764,52 +1704,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1834,18 +1798,15 @@ - + - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r + + topModel_HlyIIRpart_module_sub__ka + topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__nr + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1864,30 +1825,24 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__kao_f + topModel_HlyIIRpart_module_sub__kao_r + topModel_HlyIIRpart_module_sub__nr @@ -1905,52 +1860,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1960,11 +1939,8 @@ - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - + topModel_HlyIIRpart_module_sub__pBAD + topModel_HlyIIRpart_module_sub__ko topModel_HlyIIRpart_module_sub__ko_f topModel_HlyIIRpart_module_sub__ko_r @@ -1973,18 +1949,15 @@ + 1 - - 1 + - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr + + topModel_HlyIIRpart_module_sub__ko_f + topModel_HlyIIRpart_module_sub__ko_r + topModel_HlyIIRpart_module_sub__nr @@ -2002,8 +1975,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10_bound.jani new file mode 100644 index 0000000..7eae89f --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10_bound.jani @@ -0,0 +1,3493 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" + }, + { + "name": "topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (310 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (310 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 300 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR <- topModel_AmtRpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pHlyIIR", + "value": "topModel_AmtRpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet <- topModel_HlyIIRpart_module_sub__pTet", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pTet", + "value": "topModel_HlyIIRpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD <- topModel_HlyIIRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_HlyIIRpart_module_sub__pBAD", + "value": "topModel_HlyIIRpart_module_sub__pBAD" + } + ] + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + 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null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + 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+ "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_000to101_G1_10_10.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_000to101_G1_10_10.jani new file mode 100644 index 0000000..109981f --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_000to101_G1_10_10.jani @@ -0,0 +1,4091 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 0)", + "exp": { + "left": "HlyIIR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": 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2 + }, + { + "name": "topModel_PhlFpart_module_sub__nr", + "type": "real", + "value": 30 + }, + { + "name": "topModel_PhlFpart_module_sub__ko", + "type": "real", + "value": 0.05 + }, + { + "name": "topModel_PhlFpart_module_sub__kb", + "type": "real", + "value": 0.0001 + }, + { + "name": "topModel_PhlFpart_module_sub__ng", + "type": "real", + "value": 2 + }, + { + "name": "topModel_PhlFpart_module_sub__np", + "type": "real", + "value": 10 + }, + { + "name": "topModel_PhlFpart_module_sub__ka", + "type": "real", + "value": 0.25 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "Circuit0x8E_LHF_000to101_G1_10_10", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "YFP_protein", + "op": "≤", + "right": 30 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 1000, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "HlyIIR_protein" + }, + { + "automaton": "LacI_protein" + }, + { + "automaton": "Ara_AraC_protein" + }, + { + "automaton": "BetI_protein" + }, + { + "automaton": "PhlF_protein" + }, + { + "automaton": "AmtR_protein" + }, + { + "automaton": "TetR_protein" + }, + { + "automaton": "YFP_protein" + }, + { + "automaton": "BM3R1_protein" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BM3R1_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml index c1e2259..7624a8a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100_bound.jani new file mode 100644 index 0000000..d59613b --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (130 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (130 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein <= (130 - 10))", + "exp": { + "left": "BetI_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "PhlF_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein - 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein > 9)", + "exp": { + "left": "PhlF_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein <= (130 - 10))", + "exp": { + "left": "PhlF_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein <= (130 - 10))", + "exp": { + "left": "PhlF_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "PhlF_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + 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0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml index c1e2259..7624a8a 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10_bound.jani new file mode 100644 index 0000000..aa1a9a1 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (130 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": 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null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 130, + "name": "BetI_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 0, + "name": "AmtR_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml index 15c5df4..e5e9615 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml @@ -1,848 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -850,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -975,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1006,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1061,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1074,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1103,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1158,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1171,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1200,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1270,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1300,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1341,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1396,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1409,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1438,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1493,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1506,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1535,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1590,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1603,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1632,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1687,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1700,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1729,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1799,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1829,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1870,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1925,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1938,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1967,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2022,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2035,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2064,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2095,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111_bound.jani new file mode 100644 index 0000000..823f7fe --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": 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"comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (130 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 120 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": 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"name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 0)", + "exp": { + "left": "HlyIIR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + 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"synchronise": [ + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 130, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml index 15c5df4..e5e9615 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml @@ -1,848 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -850,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -882,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -913,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -944,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -975,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1006,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1061,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1074,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1103,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1158,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1171,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1200,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1270,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1300,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1341,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1396,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1409,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1438,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1493,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1506,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1535,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1590,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1603,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1632,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1687,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1700,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1729,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1799,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1829,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1870,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1925,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1938,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1967,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2022,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2035,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2064,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2095,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.jani new file mode 100644 index 0000000..04f1fd2 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.jani @@ -0,0 +1,4091 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 0)", + "exp": { + "left": "HlyIIR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "LacI_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Ara_AraC_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "PhlF_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein - 10)", + 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"rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "LacI_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Ara_AraC_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + 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"topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + 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topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "LacI_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Ara_AraC_protein", + "variables": [] + }, + { + "edges": [ + { + 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"automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BM3R1_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 250, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 250, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml index b1e2fea..5176ef2 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010_bound.jani new file mode 100644 index 0000000..a5c0696 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (100 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": 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"action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein <= (100 - 10))", + "exp": { + "left": "AmtR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "AmtR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "YFP_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "YFP_protein <- (YFP_protein - 10)", + "ref": "YFP_protein", + "value": { + "left": "YFP_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + 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a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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+ + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111_bound.jani new file mode 100644 index 0000000..17b5a35 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein <= (100 - 10))", + "exp": { + "left": "HlyIIR_protein", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + 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"topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml index d9f22e7..d77b8ff 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.jani new file mode 100644 index 0000000..9562ba4 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.jani @@ -0,0 +1,4091 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + 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+ "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 0)", + "exp": { + "left": "HlyIIR_protein", + "op": "≥", + "right": 0 + } + }, + 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"rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": 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"rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + 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b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.jani @@ -0,0 +1,4091 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": 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+ { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": 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"automaton": "PhlF_protein" + }, + { + "automaton": "AmtR_protein" + }, + { + "automaton": "TetR_protein" + }, + { + "automaton": "YFP_protein" + }, + { + "automaton": "BM3R1_protein" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BM3R1_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 250, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 250, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml index c3dd077..4e93765 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml index c3dd077..4e93765 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10_bound.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10_bound.jani new file mode 100644 index 0000000..2035da9 --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10_bound.jani @@ -0,0 +1,3732 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": 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"transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": 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"lower": 0, + "lower-exclusive": false, + "upper": 1000, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "HlyIIR_protein" + }, + { + "automaton": "LacI_protein" + }, + { + "automaton": "Ara_AraC_protein" + }, + { + "automaton": "BetI_protein" + }, + { + "automaton": "PhlF_protein" + }, + { + "automaton": "AmtR_protein" + }, + { + "automaton": "TetR_protein" + }, + { + "automaton": "YFP_protein" + }, + { + "automaton": "BM3R1_protein" + }, + { + "automaton": "topModel_BetIpart_module_sub__pTet" + }, + { + "automaton": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "automaton": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "automaton": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "automaton": "topModel_YFPpart_module_sub__pBetI" + }, + { + "automaton": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "automaton": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pTac" + }, + { + "automaton": "topModel_PhlFpart_module_sub__pAmtR" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "AmtR_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + "AmtR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "AmtR_degradation_interaction" + ] + }, + { + "result": "BM3R1_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BM3R1_degradation_interaction" + ] + }, + { + "result": "BetI_degradation_interaction", + "synchronise": [ + null, + null, + null, + "BetI_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "BetI_degradation_interaction" + ] + }, + { + "result": "HlyIIR_degradation_interaction", + "synchronise": [ + "HlyIIR_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "HlyIIR_degradation_interaction" + ] + }, + { + "result": "PhlF_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + "PhlF_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "PhlF_degradation_interaction" + ] + }, + { + "result": "YFP_degradation_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "YFP_degradation_interaction" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + ] + }, + { + "result": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + ] + }, + { + "result": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "synchronise": [ + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + ] + }, + { + "result": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "synchronise": [ + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + ] + }, + { + "result": "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + ] + }, + { + "result": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + ] + }, + { + "result": "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + "synchronise": [ + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1", + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + null, + "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_HlyIIR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 250, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 250, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml index e1e4c89..229429f 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.jani b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.jani new file mode 100644 index 0000000..6decbca --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.jani @@ -0,0 +1,4091 @@ +{ + "actions": [ + { + "name": "AmtR_degradation_interaction" + }, + { + "name": "BM3R1_degradation_interaction" + }, + { + "name": "BetI_degradation_interaction" + }, + { + "name": "HlyIIR_degradation_interaction" + }, + { + "name": "PhlF_degradation_interaction" + }, + { + "name": "YFP_degradation_interaction" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" + }, + { + "name": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_0" + }, + { + "name": "topModel_BetIpart_module_sub__BetI_protein_interaction_1" + }, + { + "name": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction" + }, + { + "name": "topModel_Inverter2_module_sub__BM3R1_protein_interaction" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" + }, + { + "name": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_0" + }, + { + "name": "topModel_YFPpart_module_sub__YFP_protein_interaction_1" + } + ], + "automata": [ + { + "edges": [ + { + "action": "HlyIIR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein - 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein > 9)", + "exp": { + "left": "HlyIIR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_Inverter1_module_sub__HlyIIR_protein_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "HlyIIR_protein <- (HlyIIR_protein + 10)", + "ref": "HlyIIR_protein", + "value": { + "left": "HlyIIR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(HlyIIR_protein >= 0)", + "exp": { + "left": "HlyIIR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_HlyIIR_protein <- HlyIIR_protein", + "ref": "rewardmodel_HlyIIR_protein", + "value": "HlyIIR_protein" + }, + { + "comment": "rewardmodel_LacI_protein <- LacI_protein", + "ref": "rewardmodel_LacI_protein", + "value": "LacI_protein" + }, + { + "comment": "rewardmodel_Ara_AraC_protein <- Ara_AraC_protein", + "ref": "rewardmodel_Ara_AraC_protein", + "value": "Ara_AraC_protein" + }, + { + "comment": "rewardmodel_BetI_protein <- BetI_protein", + "ref": "rewardmodel_BetI_protein", + "value": "BetI_protein" + }, + { + "comment": "rewardmodel_PhlF_protein <- PhlF_protein", + "ref": "rewardmodel_PhlF_protein", + "value": "PhlF_protein" + }, + { + "comment": "rewardmodel_AmtR_protein <- AmtR_protein", + "ref": "rewardmodel_AmtR_protein", + "value": "AmtR_protein" + }, + { + "comment": "rewardmodel_TetR_protein <- TetR_protein", + "ref": "rewardmodel_TetR_protein", + "value": "TetR_protein" + }, + { + "comment": "rewardmodel_YFP_protein <- YFP_protein", + "ref": "rewardmodel_YFP_protein", + "value": "YFP_protein" + }, + { + "comment": "rewardmodel_BM3R1_protein <- BM3R1_protein", + "ref": "rewardmodel_BM3R1_protein", + "value": "BM3R1_protein" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pTet <- topModel_BetIpart_module_sub__pTet", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "value": "topModel_BetIpart_module_sub__pTet" + }, + { + "comment": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR <- topModel_BetIpart_module_sub__pHlyIIR", + "ref": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "value": "topModel_BetIpart_module_sub__pHlyIIR" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1 <- topModel_AmtRpart_module_sub__pBM3R1", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "value": "topModel_AmtRpart_module_sub__pBM3R1" + }, + { + "comment": "rewardmodel_topModel_AmtRpart_module_sub__pBAD <- topModel_AmtRpart_module_sub__pBAD", + "ref": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "value": "topModel_AmtRpart_module_sub__pBAD" + }, + { + "comment": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc <- topModel_Inverter2_module_sub__Inverter2_fc", + "ref": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "value": "topModel_Inverter2_module_sub__Inverter2_fc" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pBetI <- topModel_YFPpart_module_sub__pBetI", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "value": "topModel_YFPpart_module_sub__pBetI" + }, + { + "comment": "rewardmodel_topModel_YFPpart_module_sub__pPhlF <- topModel_YFPpart_module_sub__pPhlF", + "ref": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "value": "topModel_YFPpart_module_sub__pPhlF" + }, + { + "comment": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc <- topModel_Inverter1_module_sub__Inverter1_fc", + "ref": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "value": "topModel_Inverter1_module_sub__Inverter1_fc" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pTac <- topModel_PhlFpart_module_sub__pTac", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "value": "topModel_PhlFpart_module_sub__pTac" + }, + { + "comment": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR <- topModel_PhlFpart_module_sub__pAmtR", + "ref": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "value": "topModel_PhlFpart_module_sub__pAmtR" + } + ] + } + ], + "name": "HlyIIR_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "LacI_protein", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "Ara_AraC_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "BetI_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein - 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein > 9)", + "exp": { + "left": "BetI_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_BetIpart_module_sub__BetI_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "BetI_protein <- (BetI_protein + 10)", + "ref": "BetI_protein", + "value": { + "left": "BetI_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(BetI_protein >= 0)", + "exp": { + "left": "BetI_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "BetI_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "PhlF_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein - 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein > 9)", + "exp": { + "left": "PhlF_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein >= 0)", + "exp": { + "left": "PhlF_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_PhlFpart_module_sub__PhlF_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "PhlF_protein <- (PhlF_protein + 10)", + "ref": "PhlF_protein", + "value": { + "left": "PhlF_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(PhlF_protein >= 0)", + "exp": { + "left": "PhlF_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "PhlF_protein", + "variables": [] + }, + { + "edges": [ + { + "action": "AmtR_degradation_interaction", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein - 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "-", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein > 9)", + "exp": { + "left": "AmtR_protein", + "op": ">", + "right": 9 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_0", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": "AmtR_protein", + "op": "≥", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "topModel_AmtRpart_module_sub__AmtR_protein_interaction_1", + "destinations": [ + { + "assignments": [ + { + "comment": "AmtR_protein <- (AmtR_protein + 10)", + "ref": "AmtR_protein", + "value": { + "left": "AmtR_protein", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AmtR_protein >= 0)", + "exp": { + "left": 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"rewardmodel_LacI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_Ara_AraC_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BetI_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_PhlF_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_AmtR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_YFP_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_BM3R1_protein", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pTet", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_BetIpart_module_sub__pHlyIIR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBM3R1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_AmtRpart_module_sub__pBAD", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter2_module_sub__Inverter2_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pBetI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_YFPpart_module_sub__pPhlF", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_Inverter1_module_sub__Inverter1_fc", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pTac", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_topModel_PhlFpart_module_sub__pAmtR", + "transient": true, + "type": "real" + }, + { + "initial-value": 250, + "name": "HlyIIR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "LacI_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "Ara_AraC_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BetI_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "PhlF_protein", + "type": "int" + }, + { + "initial-value": 250, + "name": "AmtR_protein", + "type": "int" + }, + { + "initial-value": 60, + "name": "TetR_protein", + "type": "int" + }, + { + "initial-value": 0, + "name": "YFP_protein", + "type": "int" + }, + { + "initial-value": 70, + "name": "BM3R1_protein", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pTet", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_BetIpart_module_sub__pHlyIIR", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBM3R1", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_AmtRpart_module_sub__pBAD", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter2_module_sub__Inverter2_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pBetI", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_YFPpart_module_sub__pPhlF", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_Inverter1_module_sub__Inverter1_fc", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pTac", + "type": "int" + }, + { + "initial-value": 2, + "name": "topModel_PhlFpart_module_sub__pAmtR", + "type": "int" + } + ] +} diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml index e1e4c89..229429f 100644 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml +++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml @@ -1,849 +1,571 @@ - - - + + + - + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - + + - + + + + - + + + + - + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -851,31 +573,41 @@ 30 - - - - + + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -883,30 +615,40 @@ BM3R1_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -914,30 +656,40 @@ PhlF_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -945,30 +697,40 @@ YFP_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -976,30 +738,40 @@ HlyIIR_protein - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -1007,52 +779,76 @@ BetI_protein - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1062,11 +858,8 @@ - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pTet + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1075,18 +868,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1104,52 +894,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1159,11 +973,8 @@ - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - + topModel_BetIpart_module_sub__pHlyIIR + topModel_BetIpart_module_sub__ko topModel_BetIpart_module_sub__ko_f topModel_BetIpart_module_sub__ko_r @@ -1172,18 +983,15 @@ + 1 - - 1 + - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr + + topModel_BetIpart_module_sub__ko_f + topModel_BetIpart_module_sub__ko_r + topModel_BetIpart_module_sub__nr @@ -1201,52 +1009,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1271,18 +1103,15 @@ - + - - - - topModel_AmtRpart_module_sub__ka - topModel_AmtRpart_module_sub__kao_f - - topModel_AmtRpart_module_sub__kao_r + + topModel_AmtRpart_module_sub__ka + topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__nr + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1301,30 +1130,24 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr - - - - topModel_AmtRpart_module_sub__kao_f - topModel_AmtRpart_module_sub__kao_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__kao_f + topModel_AmtRpart_module_sub__kao_r + topModel_AmtRpart_module_sub__nr @@ -1342,52 +1165,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1397,11 +1244,8 @@ - - - topModel_AmtRpart_module_sub__pBAD - topModel_AmtRpart_module_sub__ko - + topModel_AmtRpart_module_sub__pBAD + topModel_AmtRpart_module_sub__ko topModel_AmtRpart_module_sub__ko_f topModel_AmtRpart_module_sub__ko_r @@ -1410,18 +1254,15 @@ + 1 - - 1 + - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr + + topModel_AmtRpart_module_sub__ko_f + topModel_AmtRpart_module_sub__ko_r + topModel_AmtRpart_module_sub__nr @@ -1439,52 +1280,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1494,11 +1357,8 @@ - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - + topModel_Inverter2_module_sub__Inverter2_fc + topModel_Inverter2_module_sub__ko topModel_Inverter2_module_sub__ko_f topModel_Inverter2_module_sub__ko_r @@ -1507,18 +1367,15 @@ + 1 - - 1 + - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr + + topModel_Inverter2_module_sub__ko_f + topModel_Inverter2_module_sub__ko_r + topModel_Inverter2_module_sub__nr @@ -1536,52 +1393,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1591,11 +1472,8 @@ - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pBetI + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1604,18 +1482,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1633,52 +1508,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1688,11 +1587,8 @@ - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - + topModel_YFPpart_module_sub__pPhlF + topModel_YFPpart_module_sub__ko topModel_YFPpart_module_sub__ko_f topModel_YFPpart_module_sub__ko_r @@ -1701,18 +1597,15 @@ + 1 - - 1 + - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr + + topModel_YFPpart_module_sub__ko_f + topModel_YFPpart_module_sub__ko_r + topModel_YFPpart_module_sub__nr @@ -1730,52 +1623,74 @@ - - - + + + - + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + - - + + - + + + + + + - - - + + + @@ -1800,18 +1715,15 @@ - + - - - - topModel_Inverter1_module_sub__ka - topModel_Inverter1_module_sub__kao_f - - topModel_Inverter1_module_sub__kao_r + + topModel_Inverter1_module_sub__ka + topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__nr + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1830,30 +1742,24 @@ + 1 - - 1 + - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__ko_f + topModel_Inverter1_module_sub__ko_r + topModel_Inverter1_module_sub__nr - - - - topModel_Inverter1_module_sub__kao_f - topModel_Inverter1_module_sub__kao_r - - topModel_Inverter1_module_sub__nr + + topModel_Inverter1_module_sub__kao_f + topModel_Inverter1_module_sub__kao_r + topModel_Inverter1_module_sub__nr @@ -1871,52 +1777,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -1926,11 +1856,8 @@ - - - topModel_PhlFpart_module_sub__pTac - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pTac + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -1939,18 +1866,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -1968,52 +1892,76 @@ - - - + + + - + + + + + + + + - - + + - + + + + + + - - - - + + + + - + + + + + + + + - - + + - + + + + + + - - - + + + @@ -2023,11 +1971,8 @@ - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - + topModel_PhlFpart_module_sub__pAmtR + topModel_PhlFpart_module_sub__ko topModel_PhlFpart_module_sub__ko_f topModel_PhlFpart_module_sub__ko_r @@ -2036,18 +1981,15 @@ + 1 - - 1 + - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr + + topModel_PhlFpart_module_sub__ko_f + topModel_PhlFpart_module_sub__ko_r + topModel_PhlFpart_module_sub__nr @@ -2065,30 +2007,40 @@ - - - + + + - + + + + + + - - + + - + + + + + + - - - + + + @@ -2096,8 +2048,8 @@ AmtR_protein - - - - + + + + diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm deleted file mode 100644 index b8b47f0..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml deleted file mode 100644 index b91be7e..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm deleted file mode 100644 index 35f11c3..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_000to011.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm deleted file mode 100644 index b327658..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml deleted file mode 100644 index b91be7e..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm deleted file mode 100644 index 35f11c3..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_000to011.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm deleted file mode 100644 index 1c01cde..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml deleted file mode 100644 index cffad67..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm deleted file mode 100644 index 4562659..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_000to101.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm deleted file mode 100644 index af52709..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml deleted file mode 100644 index cffad67..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm deleted file mode 100644 index 4562659..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_000to101.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm deleted file mode 100644 index ce8174b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml deleted file mode 100644 index 151ce56..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm deleted file mode 100644 index dc5baca..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_011to000.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm deleted file mode 100644 index 892e1f6..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 70; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 0; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml deleted file mode 100644 index 52e2152..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml +++ /dev/null @@ -1,2619 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm deleted file mode 100644 index ec11386..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm +++ /dev/null @@ -1,442 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_010to100.xml - -// EXPECTED PROBABILITY: 47.307% -// STAMINA PROBABILITY: 0.9999999999998181 - 1.0 - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm deleted file mode 100644 index dfa1a4a..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 70; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 0; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml deleted file mode 100644 index 52e2152..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml +++ /dev/null @@ -1,2619 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm deleted file mode 100644 index ec11386..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm +++ /dev/null @@ -1,442 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_010to100.xml - -// EXPECTED PROBABILITY: 47.307% -// STAMINA PROBABILITY: 0.9999999999998181 - 1.0 - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm deleted file mode 100644 index 35b03dd..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml deleted file mode 100644 index 815e0b1..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm deleted file mode 100644 index c13ad84..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_011to101.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm deleted file mode 100644 index 0910313..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 70; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 0; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml deleted file mode 100644 index f0d89a2..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm deleted file mode 100644 index 2bd631c..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_010to111.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm deleted file mode 100644 index 66ebd53..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 70; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 0; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml deleted file mode 100644 index f0d89a2..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm deleted file mode 100644 index 2bd631c..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_010to111.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm deleted file mode 100644 index af120b9..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml deleted file mode 100644 index 151ce56..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm deleted file mode 100644 index dc5baca..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_011to000.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm deleted file mode 100644 index f438e87..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 0; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 70; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 0; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml deleted file mode 100644 index 815e0b1..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm deleted file mode 100644 index c13ad84..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_011to101.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm deleted file mode 100644 index 6b14d82..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml deleted file mode 100644 index 59d639c..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm deleted file mode 100644 index 3175604..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_100to010.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm deleted file mode 100644 index 9faa1ac..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml deleted file mode 100644 index 59d639c..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm deleted file mode 100644 index 3175604..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_100to010.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm deleted file mode 100644 index a83e9bd..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml deleted file mode 100644 index b8d47e7..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm deleted file mode 100644 index 099bf23..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_100to111.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm deleted file mode 100644 index 9a52d2b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 0; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 70; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml deleted file mode 100644 index b8d47e7..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm deleted file mode 100644 index 099bf23..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_100to111.xml - -ctmc - -const int MAX_AMOUNT = 100; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = 0; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm deleted file mode 100644 index 89f5e4b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 250; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 0; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml deleted file mode 100644 index 2e9f85f..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm deleted file mode 100644 index 543320e..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_101to000.xml - -ctmc - -const int MAX_AMOUNT = 250; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm deleted file mode 100644 index 2dd02fd..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 250; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 0; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml deleted file mode 100644 index 2e9f85f..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm deleted file mode 100644 index 543320e..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_101to000.xml - -ctmc - -const int MAX_AMOUNT = 250; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm deleted file mode 100644 index fd9eb3e..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 250; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 0; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml deleted file mode 100644 index dc200de..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm deleted file mode 100644 index d5e3fa9..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_101to011.xml - -ctmc - -const int MAX_AMOUNT = 250; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl deleted file mode 100644 index d0b751b..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl +++ /dev/null @@ -1,6 +0,0 @@ -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules - -P=? [ true U[0,1000] (YFP_protein <= 30) ] - -//P=? [ true U[0,1000] (YFP_protein < 30) ] - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm deleted file mode 100644 index 11c219d..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 250; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 70; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 60; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 0; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml deleted file mode 100644 index dc200de..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm deleted file mode 100644 index d5e3fa9..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_101to011.xml - -ctmc - -const int MAX_AMOUNT = 250; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = HIGH; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm deleted file mode 100644 index f46642d..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml deleted file mode 100644 index 8ffe3ba..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm deleted file mode 100644 index 58947b2..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm +++ /dev/null @@ -1,441 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_111to010.xml - -ctmc - -const int MAX_AMOUNT = 310; -//const int MAX_AMOUNT = 200; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters - -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm deleted file mode 100644 index 01b10e4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 60; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 0; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml deleted file mode 100644 index 8ffe3ba..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm deleted file mode 100644 index 58947b2..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm +++ /dev/null @@ -1,441 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_111to010.xml - -ctmc - -const int MAX_AMOUNT = 310; -//const int MAX_AMOUNT = 200; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = 0; -const double LacI_protein = HIGH; -const double Ara_AraC_protein = 0; - - -// Manually added parameters - -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm deleted file mode 100644 index 4d5ce58..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml deleted file mode 100644 index ff8e06a..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm deleted file mode 100644 index 5f753b7..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_111to100.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm deleted file mode 100644 index e1a2e93..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm +++ /dev/null @@ -1,456 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 7.5E-4; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate -const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate -const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count -const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate -const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count -const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate -const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate -const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count -const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production -const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate - -// Species BM3R1_protein -module BM3R1_protein - - BM3R1_protein : int init 70; - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10); - -endmodule - -// Species HlyIIR_protein -module HlyIIR_protein - - HlyIIR_protein : int init 310; - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species SrpR_protein -module SrpR_protein - - SrpR_protein : int init 0; - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10); - -endmodule - -// Species Ara_AraC_protein -module Ara_AraC_protein - - Ara_AraC_protein : int init 0; - - // Ara_AraC_protein_degradation_interaction - [Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // LacI_degradation_interaction - [LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10); - -endmodule - -// Species BetI_protein -module BetI_protein - - BetI_protein : int init 70; - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10); - -endmodule - -// Species PhlF_protein -module PhlF_protein - - PhlF_protein : int init 70; - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10); - -endmodule - -// Species AmtR_protein -module AmtR_protein - - AmtR_protein : int init 250; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // TetR_degradation_interaction - [TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : int init 2; - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : int init 2; - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : int init 2; - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : int init 2; - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : int init 2; - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : int init 2; - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: 10 SrpR_protein -> - [SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true; - - // TetR_degradation_interaction: 10 TetR_protein -> - [TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // BM3R1_degradation_interaction: 10 BM3R1_protein -> - [BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true; - - // PhlF_degradation_interaction: 10 PhlF_protein -> - [PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true; - - // YFP_degradation_interaction: 10 YFP_protein -> - [YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // LacI_degradation_interaction: 10 LacI_protein -> - [LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // HlyIIR_degradation_interaction: 10 HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true; - - // BetI_degradation_interaction: 10 BetI_protein -> - [BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> 10 PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> 10 YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true; - - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> 10 SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true; - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> 10 AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true; - - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> 10 HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true; - - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> 10 BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> 10 BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true; - - // AmtR_degradation_interaction: 10 AmtR_protein -> - [AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true; - - // Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 5: Ara_AraC_protein -rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards -// Reward 6: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 10: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml deleted file mode 100644 index ff8e06a..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml +++ /dev/null @@ -1,2620 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - YFP_protein - 30 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - SrpR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BM3R1_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - PhlF_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - HlyIIR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - BetI_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pAmtR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - SrpR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_PhlFpart_module_sub__pSrpR - topModel_PhlFpart_module_sub__ko - - topModel_PhlFpart_module_sub__ko_f - - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - 1 - - - - - topModel_PhlFpart_module_sub__ko_f - topModel_PhlFpart_module_sub__ko_r - - topModel_PhlFpart_module_sub__nr - - - - - - - - - topModel_PhlFpart_module_sub__kr_f - topModel_PhlFpart_module_sub__kr_r - - AmtR_protein - - topModel_PhlFpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pBetI - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - PhlF_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_YFPpart_module_sub__pPhlF - topModel_YFPpart_module_sub__ko - - topModel_YFPpart_module_sub__ko_f - - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - 1 - - - - - topModel_YFPpart_module_sub__ko_f - topModel_YFPpart_module_sub__ko_r - - topModel_YFPpart_module_sub__nr - - - - - - - - - topModel_YFPpart_module_sub__kr_f - topModel_YFPpart_module_sub__kr_r - - BetI_protein - - topModel_YFPpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter2_module_sub__Inverter2_fc - topModel_Inverter2_module_sub__ko - - topModel_Inverter2_module_sub__ko_f - - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter2_module_sub__ko_f - topModel_Inverter2_module_sub__ko_r - - topModel_Inverter2_module_sub__nr - - - - - - - - - topModel_Inverter2_module_sub__kr_f - topModel_Inverter2_module_sub__kr_r - - BM3R1_protein - - topModel_Inverter2_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pBAD - - - - - - - kb - - - ko_f - ko_r - - - nr - - - - - - - - ka - - - kao_f - kao_r - - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kao_f - kao_r - - nr - - - - - - - - ka_f - ka_r - - Ara_AraC_protein - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_AmtRpart_module_sub__pHlyIIR - topModel_AmtRpart_module_sub__ko - - topModel_AmtRpart_module_sub__ko_f - - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - 1 - - - - - topModel_AmtRpart_module_sub__ko_f - topModel_AmtRpart_module_sub__ko_r - - topModel_AmtRpart_module_sub__nr - - - - - - - - - topModel_AmtRpart_module_sub__kr_f - topModel_AmtRpart_module_sub__kr_r - - HlyIIR_protein - - topModel_AmtRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pTet - - - - - - - - - topModel_HlyIIRpart_module_sub__kb - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - - topModel_HlyIIRpart_module_sub__ka - topModel_HlyIIRpart_module_sub__kao_f - - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kao_f - topModel_HlyIIRpart_module_sub__kao_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - topModel_HlyIIRpart_module_sub__ka_f - topModel_HlyIIRpart_module_sub__ka_r - - Ara_AraC_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_HlyIIRpart_module_sub__pBAD - topModel_HlyIIRpart_module_sub__ko - - topModel_HlyIIRpart_module_sub__ko_f - - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - 1 - - - - - topModel_HlyIIRpart_module_sub__ko_f - topModel_HlyIIRpart_module_sub__ko_r - - topModel_HlyIIRpart_module_sub__nr - - - - - - - - - topModel_HlyIIRpart_module_sub__kr_f - topModel_HlyIIRpart_module_sub__kr_r - - TetR_protein - - topModel_HlyIIRpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_Inverter1_module_sub__Inverter1_fc - topModel_Inverter1_module_sub__ko - - topModel_Inverter1_module_sub__ko_f - - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - 1 - - - - - topModel_Inverter1_module_sub__ko_f - topModel_Inverter1_module_sub__ko_r - - topModel_Inverter1_module_sub__nr - - - - - - - - - topModel_Inverter1_module_sub__kr_f - topModel_Inverter1_module_sub__kr_r - - LacI_protein - - topModel_Inverter1_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pHlyIIR - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - HlyIIR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topModel_BetIpart_module_sub__pTet - topModel_BetIpart_module_sub__ko - - topModel_BetIpart_module_sub__ko_f - - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - 1 - - - - - topModel_BetIpart_module_sub__ko_f - topModel_BetIpart_module_sub__ko_r - - topModel_BetIpart_module_sub__nr - - - - - - - - - topModel_BetIpart_module_sub__kr_f - topModel_BetIpart_module_sub__kr_r - - TetR_protein - - topModel_BetIpart_module_sub__nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - AmtR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - Ara_AraC_protein - - - - - - - diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm deleted file mode 100644 index 5f753b7..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm +++ /dev/null @@ -1,439 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: Circuit0x8E_TI_111to100.xml - -ctmc - -const int MAX_AMOUNT = 310; - -// Compartment size -const double Cell = 1.0; - -// Model inputs -const HIGH = 60; -const double TetR_protein = HIGH; -const double LacI_protein = 0; -const double Ara_AraC_protein = 0; - - -// Manually added parameters -const double kb = 0.0001; -const double ko_f = 0.05; -const double ko_r = 1; -const double nr = 30; -const double ka = 0.25; -const double ka_f = 0.25; -const double ka_r = 1; - -const double kao_f = 1; -const double kao_r = 1; - -// Model parameters -const double kd = 0.00075; // kd -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double nc = 2; // nc -const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f -const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r -const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f -const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r -const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f -const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r -const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f -const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r -const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc -const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr -const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko -const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb -const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng -const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np -const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka -const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f -const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r -const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f -const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r -const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f -const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r -const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f -const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r -const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc -const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr -const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko -const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb -const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng -const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np -const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka -const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f -const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r -const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f -const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r -const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f -const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r -const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f -const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r -const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc -const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr -const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko -const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb -const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng -const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np -const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka -const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f -const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r -const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f -const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r -const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f -const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r -const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f -const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r -const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc -const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr -const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko -const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb -const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng -const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np -const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka -const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f -const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r -const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f -const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r -const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f -const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r -const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f -const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r -const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc -const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr -const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko -const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb -const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng -const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np -const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka -const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f -const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r -const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f -const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r -const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f -const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r -const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f -const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r -const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc -const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr -const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko -const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb -const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng -const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np -const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka -const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f -const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r -const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f -const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r -const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f -const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r -const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f -const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r -const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc -const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr -const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko -const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb -const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng -const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np -const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka - -// Species BM3R1_protein -const int BM3R1_protein_MAX = MAX_AMOUNT; -module BM3R1_protein - - BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70 - - // BM3R1_degradation_interaction - [BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10); - // topModel_Inverter1_module_sub__BM3R1_protein_interaction - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10); - -endmodule - -// Species HlyIIR_protein -const int HlyIIR_protein_MAX = MAX_AMOUNT; -module HlyIIR_protein - - HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310 - - // HlyIIR_degradation_interaction - [HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1 - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10); - -endmodule - -// Species YFP_protein -const int YFP_protein_MAX = MAX_AMOUNT; -module YFP_protein - - YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0 - - // YFP_degradation_interaction - [YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_0 - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - // topModel_YFPpart_module_sub__YFP_protein_interaction_1 - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10); - -endmodule - -// Species SrpR_protein -const int SrpR_protein_MAX = MAX_AMOUNT; -module SrpR_protein - - SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0 - - // SrpR_degradation_interaction - [SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10); - // topModel_Inverter2_module_sub__SrpR_protein_interaction - [topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10); - -endmodule - -// Species BetI_protein -const int BetI_protein_MAX = MAX_AMOUNT; -module BetI_protein - - BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70 - - // BetI_degradation_interaction - [BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_0 - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - // topModel_BetIpart_module_sub__BetI_protein_interaction_1 - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10); - -endmodule - -// Species PhlF_protein -const int PhlF_protein_MAX = MAX_AMOUNT; -module PhlF_protein - - PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70 - - // PhlF_degradation_interaction - [PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1 - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10); - -endmodule - -// Species AmtR_protein -const int AmtR_protein_MAX = MAX_AMOUNT; -module AmtR_protein - - AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250 - - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1 - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10); - // AmtR_degradation_interaction - [AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10); - -endmodule - -// Species topModel_PhlFpart_module_sub__pAmtR -const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pAmtR - - topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_PhlFpart_module_sub__pSrpR -const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT; -module topModel_PhlFpart_module_sub__pSrpR - - topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pBetI -const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pBetI - - topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_YFPpart_module_sub__pPhlF -const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT; -module topModel_YFPpart_module_sub__pPhlF - - topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter2_module_sub__Inverter2_fc -const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT; -module topModel_Inverter2_module_sub__Inverter2_fc - - topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pBAD -const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pBAD - - topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_AmtRpart_module_sub__pHlyIIR -const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_AmtRpart_module_sub__pHlyIIR - - topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pTet -const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pTet - - topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_HlyIIRpart_module_sub__pBAD -const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT; -module topModel_HlyIIRpart_module_sub__pBAD - - topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_Inverter1_module_sub__Inverter1_fc -const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT; -module topModel_Inverter1_module_sub__Inverter1_fc - - topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pHlyIIR -const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pHlyIIR - - topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species topModel_BetIpart_module_sub__pTet -const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT; -module topModel_BetIpart_module_sub__pTet - - topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // SrpR_degradation_interaction: SrpR_protein -> - [SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true; - // TetR_degradation_interaction: TetR_protein -> - [TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true; - // BM3R1_degradation_interaction: BM3R1_protein -> - [BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true; - // PhlF_degradation_interaction: PhlF_protein -> - [PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true; - // YFP_degradation_interaction: YFP_protein -> - [YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true; - // LacI_degradation_interaction: LacI_protein -> - [LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true; - // HlyIIR_degradation_interaction: HlyIIR_protein -> - [HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true; - // BetI_degradation_interaction: BetI_protein -> - [BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein - [topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein - [topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true; - // topModel_Inverter2_module_sub__SrpR_protein_interaction: -> SrpR_protein - [topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true; - // topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein - [topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true; - // topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein - [topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true; - // topModel_Inverter1_module_sub__BM3R1_protein_interaction: -> BM3R1_protein - [topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein - [topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true; - // AmtR_degradation_interaction: AmtR_protein -> - [AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true; - // Ara_AraC_protein_degradation_interaction: Ara_AraC_protein -> - [Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: BM3R1_protein -rewards "BM3R1_protein" true : BM3R1_protein; endrewards -// Reward 2: HlyIIR_protein -rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: SrpR_protein -rewards "SrpR_protein" true : SrpR_protein; endrewards -// Reward 7: BetI_protein -rewards "BetI_protein" true : BetI_protein; endrewards -// Reward 8: PhlF_protein -rewards "PhlF_protein" true : PhlF_protein; endrewards -// Reward 9: AmtR_protein -rewards "AmtR_protein" true : AmtR_protein; endrewards -// Reward 11: topModel_PhlFpart_module_sub__pAmtR -rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards -// Reward 12: topModel_PhlFpart_module_sub__pSrpR -rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards -// Reward 13: topModel_YFPpart_module_sub__pBetI -rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards -// Reward 14: topModel_YFPpart_module_sub__pPhlF -rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards -// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc -rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards -// Reward 16: topModel_AmtRpart_module_sub__pBAD -rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards -// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR -rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards -// Reward 18: topModel_HlyIIRpart_module_sub__pTet -rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards -// Reward 19: topModel_HlyIIRpart_module_sub__pBAD -rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards -// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc -rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards -// Reward 21: topModel_BetIpart_module_sub__pHlyIIR -rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards -// Reward 22: topModel_BetIpart_module_sub__pTet -rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl deleted file mode 100644 index 46fa7d4..0000000 --- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl +++ /dev/null @@ -1,4 +0,0 @@ - -// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules - -P=? [ true U[0,1000] (YFP_protein >= 10) ] diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.jani b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.jani new file mode 100644 index 0000000..1f56c16 --- /dev/null +++ b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.jani @@ -0,0 +1,1129 @@ +{ + "actions": [ + { + "name": "Degradation_AraC" + }, + { + "name": "Degradation_LacI" + }, + { + "name": "Production_P1" + }, + { + "name": "Production_P2" + } + ], + "automata": [ + { + "edges": [ + { + "action": "Degradation_AraC", + "destinations": [ + { + "assignments": [ + { + "comment": "AraC <- (AraC - 1)", + "ref": "AraC", + "value": { + "left": "AraC", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AraC > 0)", + "exp": { + "left": "AraC", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Production_P2", + "destinations": [ + { + "assignments": [ + { + "comment": "AraC <- (AraC + 10)", + "ref": "AraC", + "value": { + "left": "AraC", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(AraC <= (100 - 10))", + "exp": { + "left": "AraC", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l", + "transient-values": [ + { + "comment": "rewardmodel_AraC <- AraC", + "ref": "rewardmodel_AraC", + "value": "AraC" + }, + { + "comment": "rewardmodel_LacI <- LacI", + "ref": "rewardmodel_LacI", + "value": "LacI" + }, + { + "comment": "rewardmodel_P1 <- P1", + "ref": "rewardmodel_P1", + "value": "P1" + }, + { + "comment": "rewardmodel_P2 <- P2", + "ref": "rewardmodel_P2", + "value": "P2" + } + ] + } + ], + "name": "AraC", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_LacI", + "destinations": [ + { + "assignments": [ + { + "comment": "LacI <- (LacI - 1)", + "ref": "LacI", + "value": { + "left": "LacI", + "op": "-", + "right": 1 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(LacI > 0)", + "exp": { + "left": "LacI", + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + }, + { + "action": "Production_P1", + "destinations": [ + { + "assignments": [ + { + "comment": "LacI <- (LacI + 10)", + "ref": "LacI", + "value": { + "left": "LacI", + "op": "+", + "right": 10 + } + } + ], + "location": "l", + "probability": { + "comment": "(1 / 1)", + "exp": 1 + } + } + ], + "guard": { + "comment": "(LacI <= (100 - 10))", + "exp": { + "left": "LacI", + "op": "≤", + "right": 90 + } + }, + "location": "l", + "rate": { + "comment": "1", + "exp": 1 + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "LacI", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "P1", + "variables": [] + }, + { + "edges": [], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "P2", + "variables": [] + }, + { + "edges": [ + { + "action": "Degradation_AraC", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((3/400 * AraC) / (3/400 * AraC))", + "exp": { + "left": { + "left": 0.0075, + "op": "*", + "right": "AraC" + }, + "op": "/", + "right": { + "left": 0.0075, + "op": "*", + "right": "AraC" + } + } + } + } + ], + "guard": { + "comment": "((3/400 * AraC) > 0)", + "exp": { + "left": { + "left": 0.0075, + "op": "*", + "right": "AraC" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(3/400 * AraC)", + "exp": { + "left": 0.0075, + "op": "*", + "right": "AraC" + } + } + }, + { + "action": "Degradation_LacI", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "((3/400 * LacI) / (3/400 * LacI))", + "exp": { + "left": { + "left": 0.0075, + "op": "*", + "right": "LacI" + }, + "op": "/", + "right": { + "left": 0.0075, + "op": "*", + "right": "LacI" + } + } + } + } + ], + "guard": { + "comment": "((3/400 * LacI) > 0)", + "exp": { + "left": { + "left": 0.0075, + "op": "*", + "right": "LacI" + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "(3/400 * LacI)", + "exp": { + "left": 0.0075, + "op": "*", + "right": "LacI" + } + } + }, + { + "action": "Production_P1", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((P1 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))) / ((P1 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))))", + "exp": { + "left": { + "left": { + "left": "P1", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "/", + "right": { + "left": { + "left": "P1", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + } + } + } + } + ], + "guard": { + "comment": "(((P1 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))) > 0)", + "exp": { + "left": { + "left": { + "left": "P1", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((P1 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2)))", + "exp": { + "left": { + "left": "P1", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + } + } + }, + { + "action": "Production_P2", + "destinations": [ + { + "location": "l", + "probability": { + "comment": "(((P2 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))) / ((P2 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))))", + "exp": { + "left": { + "left": { + "left": "P2", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "/", + "right": { + "left": { + "left": "P2", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + } + } + } + } + ], + "guard": { + "comment": "(((P2 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2))) > 0)", + "exp": { + "left": { + "left": { + "left": "P2", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": ">", + "right": 0 + } + }, + "location": "l", + "rate": { + "comment": "((P2 * (((1/10000 * (33/1000 / 1)) * 100) + (((1/4 * (1 / 1)) * 100) * (((33/10000 / 1) * AraC) ^ 2)))) / (((1 + ((33/1000 / 1) * 100)) + (((1 / 1) * 100) * (((33/10000 / 1) * AraC) ^ 2))) + (((1/2 / 1) * LacI) ^ 2)))", + "exp": { + "left": { + "left": "P2", + "op": "*", + "right": { + "left": 0.00033, + "op": "+", + "right": { + "left": 25, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + } + }, + "op": "/", + "right": { + "left": { + "left": 4.3, + "op": "+", + "right": { + "left": 100, + "op": "*", + "right": { + "left": { + "left": 0.0033, + "op": "*", + "right": "AraC" + }, + "op": "pow", + "right": 2 + } + } + }, + "op": "+", + "right": { + "left": { + "left": 0.5, + "op": "*", + "right": "LacI" + }, + "op": "pow", + "right": 2 + } + } + } + } + } + ], + "initial-locations": [ + "l" + ], + "locations": [ + { + "name": "l" + } + ], + "name": "reaction_rates", + "variables": [] + } + ], + "constants": [ + { + "name": "MAX_AMOUNT", + "type": "int", + "value": 100 + }, + { + "name": "Cell", + "type": "real", + "value": 1 + }, + { + "name": "ko_r", + "type": "real", + "value": 1 + }, + { + "name": "nr", + "type": "real", + "value": 100 + }, + { + "name": "np", + "type": "real", + "value": 10 + }, + { + "name": "kr_r", + "type": "real", + "value": 1 + }, + { + "name": "ka_f", + "type": "real", + "value": 0.0033 + }, + { + "name": "kecdiff", + "type": "real", + "value": 1 + }, + { + "name": "ko", + "type": "real", + "value": 0.05 + }, + { + "name": "kmdiff_f", + "type": "real", + "value": 1 + }, + { + "name": "kecd", + "type": "real", + "value": 0.005 + }, + { + "name": "kc_r", + "type": "real", + "value": 1 + }, + { + "name": "kr_f", + "type": "real", + "value": 0.5 + }, + { + "name": "ka_r", + "type": "real", + "value": 1 + }, + { + "name": "nc", + "type": "real", + "value": 2 + }, + { + "name": "kd", + "type": "real", + "value": 0.0075 + }, + { + "name": "kao_r", + "type": "real", + "value": 1 + }, + { + "name": "kb", + "type": "real", + "value": 0.0001 + }, + { + "name": "ng", + "type": "real", + "value": 20 + }, + { + "name": "ka", + "type": "real", + "value": 0.25 + }, + { + "name": "kao_f", + "type": "real", + "value": 1 + }, + { + "name": "kmdiff_r", + "type": "real", + "value": 0.01 + }, + { + "name": "ko_f", + "type": "real", + "value": 0.033 + }, + { + "name": "kc_f", + "type": "real", + "value": 0.05 + }, + { + "name": "limit", + "type": "real", + "value": 0 + }, + { + "name": "AraC_MAX", + "type": "int", + "value": 100 + }, + { + "name": "LacI_MAX", + "type": "int", + "value": 100 + }, + { + "name": "P1_MAX", + "type": "int", + "value": 100 + }, + { + "name": "P2_MAX", + "type": "int", + "value": 100 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "Dual_Feedback_Oscillator", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "AraC", + "op": "≥", + "right": 2 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "AraC" + }, + { + "automaton": "LacI" + }, + { + "automaton": "P1" + }, + { + "automaton": "P2" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Degradation_AraC", + "synchronise": [ + "Degradation_AraC", + null, + null, + null, + "Degradation_AraC" + ] + }, + { + "result": "Degradation_LacI", + "synchronise": [ + null, + "Degradation_LacI", + null, + null, + "Degradation_LacI" + ] + }, + { + "result": "Production_P1", + "synchronise": [ + null, + "Production_P1", + null, + null, + "Production_P1" + ] + }, + { + "result": "Production_P2", + "synchronise": [ + "Production_P2", + null, + null, + null, + "Production_P2" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_AraC", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P2", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "AraC", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "LacI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 20, + "name": "P1", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 20, + "name": "P2", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + } + ] +} diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.props b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.props new file mode 100644 index 0000000..7d417e3 --- /dev/null +++ b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.props @@ -0,0 +1 @@ +P=? [ true U[0,50] (AraC >= 2) ] diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml index 3983833..d2b7aba 100755 --- a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml +++ b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml @@ -1,137 +1,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + @@ -146,8 +17,8 @@ - - + + @@ -170,24 +41,8 @@ - - - - - - - - - - - - - - - - - - + + @@ -203,45 +58,44 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + St @@ -300,14 +154,14 @@ - - - - - - - - + + + + + + + + @@ -315,13 +169,13 @@ AraC - - - - - - - + + + + + + + @@ -329,18 +183,18 @@ LacI - - - - - - - - - - - - + + + + + + + + + + + + @@ -434,18 +288,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -539,9 +393,8 @@ - - - - - + + + + diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/results.txt b/GeneticCircuits/Dual_Feedback_Osscillator/Default/results.txt new file mode 100644 index 0000000..8633f3b --- /dev/null +++ b/GeneticCircuits/Dual_Feedback_Osscillator/Default/results.txt @@ -0,0 +1,2 @@ +0.07166679484071543 +0.07166679514795181 diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.props b/GeneticCircuits/Muller_C_Element/Majority/Majority.props deleted file mode 100644 index c1cb805..0000000 --- a/GeneticCircuits/Muller_C_Element/Majority/Majority.props +++ /dev/null @@ -1,4 +0,0 @@ -//const int T; - -// Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((EE > 40) & (CC < 20))] diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.sm b/GeneticCircuits/Muller_C_Element/Majority/Majority.sm deleted file mode 100644 index 7c8f04e..0000000 --- a/GeneticCircuits/Muller_C_Element/Majority/Majority.sm +++ /dev/null @@ -1,278 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: majority.xml - -ctmc - -const int MAX_AMOUNT = 200; - -// Compartment size -const double default = 1.0; - -// Model parameters -const double kr_f = 0.5; // kr_f -const double kr_r = 1; // kr_r -const double ka_f = 0.0033; // ka_f -const double ka_r = 1; // ka_r -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double ko_f = 0.033; // ko_f -const double ko_r = 1; // ko_r -const double kao_f = 1; // kao_f -const double kao_r = 1; // kao_r -const double kmdiff_f = 1; // kmdiff_f -const double kmdiff_r = 0.01; // kmdiff_r -const double kd = 0.0075; // kd -const double kecd = 0.005; // kecd -const double nc = 2; // nc -const double nr = 30; // nr -const double ko = 0.05; // ko -const double kb = 0.0001; // kb -const double ng = 2; // ng -const double np = 10; // np -const double ka = 0.25; // ka -const double kecdiff = 1; // kecdiff - -// Original Model did not have this module -// Species AA -const int AA_MAX = MAX_AMOUNT; -module AA - - AA : [0..AA_MAX] init 40; // Initial amount 0 - - -endmodule - -// Original Model did not have this module -// Species B -const int B_MAX = MAX_AMOUNT; -module B - - B : [0..B_MAX] init 120; // Initial amount 120 - - -endmodule - -// Species D -const int D_MAX = MAX_AMOUNT; -module D - - D : [0..D_MAX] init 200; // Initial amount 200 - - // Degradation_D - [Degradation_D] D > 0 -> (D'=D-1); - // Production_P5 - [Production_P5] D <= D_MAX-10 -> (D'=D+10); - // Production_P4 - [Production_P4] D <= D_MAX-10 -> (D'=D+10); - // Production_P6 - [Production_P6] D <= D_MAX-10 -> (D'=D+10); - -endmodule - -// Species EE -const int EE_MAX = MAX_AMOUNT; -module EE - - EE : [0..EE_MAX] init 0; // Initial amount 0 - - // Degradation_EE - [Degradation_EE] EE > 0 -> (EE'=EE-1); - // Production_P7 - [Production_P7] EE <= EE_MAX-10 -> (EE'=EE+10); - -endmodule - -// Species CC -const int CC_MAX = MAX_AMOUNT; -module CC - - CC : [0..CC_MAX] init 120; // Initial amount 120 - - // Degradation_CC - [Degradation_CC] CC > 0 -> (CC'=CC-1); - // Production_P8 - [Production_P8] CC <= CC_MAX-10 -> (CC'=CC+10); - -endmodule - -// Species Y -const int Y_MAX = MAX_AMOUNT; -module Y - - Y : [0..Y_MAX] init 0; // Initial amount 0 - - // Degradation_Y - [Degradation_Y] Y > 0 -> (Y'=Y-1); - // Production_P1 - [Production_P1] Y <= Y_MAX-10 -> (Y'=Y+10); - // Production_P3 - [Production_P3] Y <= Y_MAX-10 -> (Y'=Y+10); - -endmodule - -// Species XX -const int XX_MAX = MAX_AMOUNT; -module XX - - XX : [0..XX_MAX] init 0; // Initial amount 0 - - // Degradation_XX - [Degradation_XX] XX > 0 -> (XX'=XX-1); - // Production_P1 - [Production_P1] XX <= XX_MAX-10 -> (XX'=XX+10); - // Production_P2 - [Production_P2] XX <= XX_MAX-10 -> (XX'=XX+10); - -endmodule - -// Species Z -const int Z_MAX = MAX_AMOUNT; -module Z - - Z : [0..Z_MAX] init 0; // Initial amount 0 - - // Degradation_Z - [Degradation_Z] Z > 0 -> (Z'=Z-1); - // Production_P3 - [Production_P3] Z <= Z_MAX-10 -> (Z'=Z+10); - // Production_P2 - [Production_P2] Z <= Z_MAX-10 -> (Z'=Z+10); - -endmodule - -// Species P8 (P8) -const int P8_MAX = MAX_AMOUNT; -module P8 - - P8 : [0..P8_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P5 (P5) -const int P5_MAX = MAX_AMOUNT; -module P5 - - P5 : [0..P5_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P4 (P4) -const int P4_MAX = MAX_AMOUNT; -module P4 - - P4 : [0..P4_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P7 (P7) -const int P7_MAX = MAX_AMOUNT; -module P7 - - P7 : [0..P7_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P6 (P6) -const int P6_MAX = MAX_AMOUNT; -module P6 - - P6 : [0..P6_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P1 (P1) -const int P1_MAX = MAX_AMOUNT; -module P1 - - P1 : [0..P1_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P3 (P3) -const int P3_MAX = MAX_AMOUNT; -module P3 - - P3 : [0..P3_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P2 (P2) -const int P2_MAX = MAX_AMOUNT; -module P2 - - P2 : [0..P2_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // Degradation_D: D -> - [Degradation_D] (kd*D) > 0 -> (kd*D) : true; - // Degradation_EE: EE -> - [Degradation_EE] (kd*EE) > 0 -> (kd*EE) : true; - // Degradation_CC: CC -> - [Degradation_CC] (kd*CC) > 0 -> (kd*CC) : true; - // Degradation_Y: Y -> - [Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true; - // Degradation_XX: XX -> - [Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true; - // Degradation_Z: Z -> - [Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true; - // Production_P8: -> CC - [Production_P8] ((((P8*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*EE),nc)))) > 0 -> ((((P8*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*EE),nc)))) : true; - // Production_P5: -> D - [Production_P5] ((((P5*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> ((((P5*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Y),nc)))) : true; - // Production_P4: -> D - [Production_P4] ((((P4*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> ((((P4*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*XX),nc)))) : true; - // Production_P7: -> EE - [Production_P7] ((((P7*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> ((((P7*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) : true; - // Production_P6: -> D - [Production_P6] ((((P6*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> ((((P6*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Z),nc)))) : true; - // Production_P1: -> Y+XX - [Production_P1] ((((P1*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> ((((P1*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*AA),nc)))) : true; - // Production_P3: -> Z+Y - [Production_P3] ((((P3*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> ((((P3*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) : true; - // Production_P2: -> XX+Z - [Production_P2] ((((P2*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> ((((P2*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*B),nc)))) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: D -rewards "D" true : D; endrewards -// Reward 2: EE -rewards "EE" true : EE; endrewards -// Reward 5: CC -rewards "CC" true : CC; endrewards -// Reward 6: Y -rewards "Y" true : Y; endrewards -// Reward 7: XX -rewards "XX" true : XX; endrewards -// Reward 8: Z -rewards "Z" true : Z; endrewards -// Reward 9: P8 (P8) -rewards "P8" true : P8; endrewards -// Reward 10: P5 (P5) -rewards "P5" true : P5; endrewards -// Reward 11: P4 (P4) -rewards "P4" true : P4; endrewards -// Reward 12: P7 (P7) -rewards "P7" true : P7; endrewards -// Reward 13: P6 (P6) -rewards "P6" true : P6; endrewards -// Reward 14: P1 (P1) -rewards "P1" true : P1; endrewards -// Reward 15: P3 (P3) -rewards "P3" true : P3; endrewards -// Reward 16: P2 (P2) -rewards "P2" true : P2; endrewards diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.xml b/GeneticCircuits/Muller_C_Element/Majority/Majority.xml deleted file mode 100755 index 7620cb9..0000000 --- a/GeneticCircuits/Muller_C_Element/Majority/Majority.xml +++ /dev/null @@ -1,1228 +0,0 @@ - - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - t - - - x - - - - - - t - - - - x - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - F - - - t - 2100 - - - - - - EE - 40 - - - - CC - 20 - - - - - -

Pr=?{(true)PU[0,2100]((E greater than 40) and (C less than 20))}

- - - - - - - - - - - - - kd - D - - - - - - - - - - - - - kd - EE - - - - - - - - - - - - - kd - CC - - - - - - - - - - - - - kd - Y - - - - - - - - - - - - - kd - XX - - - - - - - - - - - - - kd - Z - - - - - - - - - - - - - - - - - - - - - - - P8 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - EE - - nc - - - - - - - - - - - - - - - - - - - - - - - - - P5 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - Y - - nc - - - - - - - - - - - - - - - - - - - - - - - - - P4 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - XX - - nc - - - - - - - - - - - - - - - - - - - - - - - - - P7 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - D - - nc - - - - - - - - - - - - - - - - - - - - - - - - - P6 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - Z - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - P1 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - AA - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - P3 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - D - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - P2 - ko - ko_f - - ko_r - - nr - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - kr_f - kr_r - - B - - nc - - - - - - - - - - - - - - t - 5000 - - - - - - 0 - - - - - - 40 - - - - - - - - - - t - 10000 - - - - - - 0 - - - - - - 40 - - - - - - - - - - t - 15000 - - - - - - 0 - - - - - - 0 - - - - - - - - - - t - 20000 - - - - - - 0 - - - - - - 0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.jani b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.jani new file mode 100644 index 0000000..5843c2e --- /dev/null +++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.jani @@ -0,0 +1,3260 @@ +{ + "actions": [ + { + "name": "Degradation_C" + }, + { + "name": "Degradation_D" + 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"lower-bound": 0, + "upper-bound": 120 + } + }, + { + "initial-value": 2, + "name": "P6", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 120 + } + }, + { + "initial-value": 2, + "name": "P7", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 120 + } + } + ] +} diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props index bc22858..7813f8a 100644 --- a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props +++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props @@ -1,4 +1,6 @@ //const int T; // Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((_E > 40) & (_C < 20))] +//"change_state" : P=? [ F<=2100 ((_E > 40) & (_C < 20))] + +P=? [ true U[0,50] (_C <= 65) ] diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml index cc64d57..20f20b8 100644 --- a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml +++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml @@ -1,754 +1,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + @@ -770,49 +24,49 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + F @@ -836,14 +90,14 @@ - - - - - - - - + + + + + + + + @@ -851,13 +105,13 @@ C - - - - - - - + + + + + + + @@ -865,13 +119,13 @@ D - - - - - - - + + + + + + + @@ -879,13 +133,13 @@ E - - - - - - - + + + + + + + @@ -893,13 +147,13 @@ X - - - - - - - + + + + + + + @@ -907,13 +161,13 @@ Y - - - - - - - + + + + + + + @@ -921,18 +175,18 @@ Z - - - - - - - - - - - - + + + + + + + + + + + + @@ -942,11 +196,8 @@ - - - P1 - ko - + P1 + ko ko_f ko_r @@ -955,18 +206,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -984,18 +232,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -1005,11 +253,8 @@ - - - P2 - ko - + P2 + ko ko_f ko_r @@ -1018,18 +263,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1047,52 +289,43 @@ - - - - - - - - - - - - + + + + + + + + + + + + + P3 + ko - - - - P3 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1110,17 +343,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1130,11 +363,8 @@ - - - P4 - ko - + P4 + ko ko_f ko_r @@ -1143,18 +373,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1172,17 +399,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1192,11 +419,8 @@ - - - P5 - ko - + P5 + ko ko_f ko_r @@ -1205,18 +429,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1234,51 +455,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P6 + ko - - - - P6 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1296,17 +508,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1316,11 +528,8 @@ - - - P7 - ko - + P7 + ko ko_f ko_r @@ -1329,18 +538,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1358,51 +564,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P8 + ko - - - - P8 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1420,8 +617,8 @@ - - - - + + + + diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt b/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt new file mode 100644 index 0000000..5d4220f --- /dev/null +++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt @@ -0,0 +1,2 @@ +0.6954372359336837 +0.6954373474398886 diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props deleted file mode 100644 index ef52047..0000000 --- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props +++ /dev/null @@ -1,2 +0,0 @@ -// Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))] diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm deleted file mode 100644 index 5d518b1..0000000 --- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm +++ /dev/null @@ -1,343 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: speedInd.xml - -ctmc - -const int MAX_AMOUNT = 200; - -// Compartment size -const double default = 1.0; - - -// Model parameters -const double kr_f = 0.5; // kr_f -const double kr_r = 1; // kr_r -const double ka_f = 0.0033; // ka_f -const double ka_r = 1; // ka_r -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double ko_f = 0.033; // ko_f -const double ko_r = 1; // ko_r -const double kao_f = 1; // kao_f -const double kao_r = 1; // kao_r -const double kmdiff_f = 1; // kmdiff_f -const double kmdiff_r = 0.01; // kmdiff_r -const double kd = 0.0075; // kd -const double kecd = 0.005; // kecd -const double nc = 2; // nc -const double nr = 30; // nr -const double ko = 0.05; // ko -const double kb = 0.0001; // kb -const double ng = 2; // ng -const double np = 10; // np -const double ka = 0.25; // ka -const double kecdiff = 1; // kecdiff - -// Species AA -const int AA_MAX = MAX_AMOUNT; -module AA - - AA : [0..AA_MAX] init 0; // Initial amount 0 - - -endmodule - -// Species B -const int B_MAX = MAX_AMOUNT; -module B - - B : [0..B_MAX] init 120; // Initial amount 120 - - -endmodule - -// Species CC -const int CC_MAX = MAX_AMOUNT; -module CC - - CC : [0..CC_MAX] init 120; // Initial amount 120 - - // Degradation_CC - [Degradation_CC] CC > 0 -> (CC'=CC-1); - // Production_P9 - [Production_P9] CC <= CC_MAX-10 -> (CC'=CC+10); - -endmodule - -// Species S1 -const int S1_MAX = MAX_AMOUNT; -module S1 - - S1 : [0..S1_MAX] init 200; // Initial amount 200 - - // Degradation_S1 - [Degradation_S1] S1 > 0 -> (S1'=S1-1); - // Production_P4 - [Production_P4] S1 <= S1_MAX-10 -> (S1'=S1+10); - // Production_P7 - [Production_P7] S1 <= S1_MAX-10 -> (S1'=S1+10); - -endmodule - -// Species S2 -const int S2_MAX = MAX_AMOUNT; -module S2 - - S2 : [0..S2_MAX] init 0; // Initial amount 0 - - // Degradation_S2 - [Degradation_S2] S2 > 0 -> (S2'=S2-1); - // Production_P8 - [Production_P8] S2 <= S2_MAX-10 -> (S2'=S2+10); - // Production_P5 - [Production_P5] S2 <= S2_MAX-10 -> (S2'=S2+10); - -endmodule - -// Species S3 -const int S3_MAX = MAX_AMOUNT; -module S3 - - S3 : [0..S3_MAX] init 120; // Initial amount 120 - - // Degradation_S3 - [Degradation_S3] S3 > 0 -> (S3'=S3-1); - // Production_P6 - [Production_P6] S3 <= S3_MAX-10 -> (S3'=S3+10); - // Production_P3 - [Production_P3] S3 <= S3_MAX-10 -> (S3'=S3+10); - -endmodule - -// Species S4 -const int S4_MAX = MAX_AMOUNT; -module S4 - - S4 : [0..S4_MAX] init 0; // Initial amount 0 - - // Degradation_S4 - [Degradation_S4] S4 > 0 -> (S4'=S4-1); - // Production_P1 - [Production_P1] S4 <= S4_MAX-10 -> (S4'=S4+10); - // Production_P2 - [Production_P2] S4 <= S4_MAX-10 -> (S4'=S4+10); - // Production_P10 - [Production_P10] S4 <= S4_MAX-10 -> (S4'=S4+10); - -endmodule - -// Species XX -const int XX_MAX = MAX_AMOUNT; -module XX - - XX : [0..XX_MAX] init 0; // Initial amount 0 - - // Degradation_XX - [Degradation_XX] XX > 0 -> (XX'=XX-1); - // Production_P1 - [Production_P1] XX <= XX_MAX-10 -> (XX'=XX+10); - -endmodule - -// Species Y -const int Y_MAX = MAX_AMOUNT; -module Y - - Y : [0..Y_MAX] init 0; // Initial amount 0 - - // Degradation_Y - [Degradation_Y] Y > 0 -> (Y'=Y-1); - // Production_P2 - [Production_P2] Y <= Y_MAX-10 -> (Y'=Y+10); - -endmodule - -// Species Z -const int Z_MAX = MAX_AMOUNT; -module Z - - Z : [0..Z_MAX] init 0; // Initial amount 0 - - // Degradation_Z - [Degradation_Z] Z > 0 -> (Z'=Z-1); - // Production_P8 - [Production_P8] Z <= Z_MAX-10 -> (Z'=Z+10); - // Production_P3 - [Production_P3] Z <= Z_MAX-10 -> (Z'=Z+10); - -endmodule - -// Species P9 -const int P9_MAX = MAX_AMOUNT; -module P9 - - P9 : [0..P9_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P8 -const int P8_MAX = MAX_AMOUNT; -module P8 - - P8 : [0..P8_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P5 -const int P5_MAX = MAX_AMOUNT; -module P5 - - P5 : [0..P5_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P4 -const int P4_MAX = MAX_AMOUNT; -module P4 - - P4 : [0..P4_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P7 -const int P7_MAX = MAX_AMOUNT; -module P7 - - P7 : [0..P7_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P6 -const int P6_MAX = MAX_AMOUNT; -module P6 - - P6 : [0..P6_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P1 -const int P1_MAX = MAX_AMOUNT; -module P1 - - P1 : [0..P1_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P3 -const int P3_MAX = MAX_AMOUNT; -module P3 - - P3 : [0..P3_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P2 -const int P2_MAX = MAX_AMOUNT; -module P2 - - P2 : [0..P2_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P10 -const int P10_MAX = MAX_AMOUNT; -module P10 - - P10 : [0..P10_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // Degradation_S3: S3 -> - [Degradation_S3] (kd*S3) > 0 -> (kd*S3) : true; - // Degradation_S4: S4 -> - [Degradation_S4] (kd*S4) > 0 -> (kd*S4) : true; - // Degradation_CC: CC -> - [Degradation_CC] (kd*CC) > 0 -> (kd*CC) : true; - // Degradation_S2: S2 -> - [Degradation_S2] (kd*S2) > 0 -> (kd*S2) : true; - // Degradation_S1: S1 -> - [Degradation_S1] (kd*S1) > 0 -> (kd*S1) : true; - // Degradation_Y: Y -> - [Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true; - // Degradation_XX: XX -> - [Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true; - // Degradation_Z: Z -> - [Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true; - // Production_P9: -> CC - [Production_P9] (((((P9*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> (((((P9*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) : true; - // Production_P8: -> Z+S2 - [Production_P8] (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S3),nc)))) > 0 -> (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S3),nc)))) : true; - // Production_P5: -> S2 - [Production_P5] (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S1),nc)))) > 0 -> (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S1),nc)))) : true; - // Production_P4: -> S1 - [Production_P4] (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) : true; - // Production_P7: -> S1 - [Production_P7] (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) : true; - // Production_P6: -> S3 - [Production_P6] (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) > 0 -> (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) : true; - // Production_P1: -> S4+XX - [Production_P1] (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) : true; - // Production_P3: -> S3+Z - [Production_P3] (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S4),nc)))) > 0 -> (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S4),nc)))) : true; - // Production_P2: -> S4+Y - [Production_P2] (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) : true; - // Production_P10: -> S4 - [Production_P10] (((((P10*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) > 0 -> (((((P10*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: AA -rewards "AA" true : AA; endrewards -// Reward 2: B -rewards "B" true : B; endrewards -// Reward 3: CC -rewards "CC" true : CC; endrewards -// Reward 4: S1 -rewards "S1" true : S1; endrewards -// Reward 5: S2 -rewards "S2" true : S2; endrewards -// Reward 6: S3 -rewards "S3" true : S3; endrewards -// Reward 7: S4 -rewards "S4" true : S4; endrewards -// Reward 8: XX -rewards "XX" true : XX; endrewards -// Reward 9: Y -rewards "Y" true : Y; endrewards -// Reward 10: Z -rewards "Z" true : Z; endrewards -// Reward 11: P9 -rewards "P9" true : P9; endrewards -// Reward 12: P8 -rewards "P8" true : P8; endrewards -// Reward 13: P5 -rewards "P5" true : P5; endrewards -// Reward 14: P4 -rewards "P4" true : P4; endrewards -// Reward 15: P7 -rewards "P7" true : P7; endrewards -// Reward 16: P6 -rewards "P6" true : P6; endrewards -// Reward 17: P1 -rewards "P1" true : P1; endrewards -// Reward 18: P3 -rewards "P3" true : P3; endrewards -// Reward 19: P2 -rewards "P2" true : P2; endrewards -// Reward 20: P10 -rewards "P10" true : P10; endrewards diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml deleted file mode 100755 index 2227d47..0000000 --- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml +++ /dev/null @@ -1,1476 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - a - - 0 - - - - - - - - t - - - x - - - - - - t - - - - x - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - F - - - t - 2100 - - - - - - S2 - 80 - - - - S3 - 20 - - - - - -

Pr=?{(true)PU[0,2100]((S2 greater than 80) and (S3 less than 20))}

 - - - - - - - - - - - - kd - S3 - - - - - - - - - - - - - kd - S4 - - - - - - - - - - - - - kd - CC - - - - - - - - - - - - - kd - S2 - - - - - - - - - - - - - kd - S1 - - - - - - - - - - - - - kd - Y - - - - - - - - - - - - - kd - XX - - - - - - - - - - - - - kd - Z - - - - - - - - - - - - - - - - - - - - - - - - - P9 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - Z - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - P8 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - S3 - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P5 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - S1 - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P4 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - XX - - nc - - - - - - - - - - - - - - - - - - - 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"type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P3", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P4", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P5", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P6", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P7", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P8", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P9", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel__X", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "_A", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 120, + "name": "B", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "S1", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 0, + "name": "S2", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "S3", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 130, + "name": "S4", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 0, + "name": "Y", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 0, + "name": "Z", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "_C", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P10", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P1", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P2", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P3", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P4", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P5", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P6", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P7", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P8", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 2, + "name": "P9", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + }, + { + "initial-value": 70, + "name": "_X", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 130 + } + } + ] +} diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props index ef52047..f8f8ec4 100644 --- a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props +++ b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props @@ -1,2 +1,4 @@ // Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))] +// "change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))] + +P=? [ true U[0,50] (S3 <= 65) ] diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml index 7b0a500..a11cc34 100644 --- a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml +++ b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml @@ -1,940 +1,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + @@ -956,53 +24,53 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + F @@ -1026,14 +94,14 @@ - - - - - - - - + + + + + + + + @@ -1041,13 +109,13 @@ S4 - - - - - - - + + + + + + + @@ -1055,13 +123,13 @@ S1 - - - - - - - + + + + + + + @@ -1069,13 +137,13 @@ Z - - - - - - - + + + + + + + @@ -1083,51 +151,42 @@ C - - - - - - - - - - - + + + + + + + + + + + + P10 + ko - - - - P10 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1145,52 +204,43 @@ - - - - - - - - - - - - + + + + + + + + + + + + + P1 + ko - - - - P1 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1208,52 +258,43 @@ - - - - - - - - - - - - + + + + + + + + + + + + + P2 + ko - - - - P2 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1271,52 +312,43 @@ - - - - - - - - - - - - + + + + + + + + + + + + + P3 + ko - - - - P3 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1334,51 +366,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P4 + ko - - - - P4 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1396,51 +419,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P5 + ko - - - - P5 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1458,51 +472,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P6 + ko - - - - P6 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1520,51 +525,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P7 + ko - - - - P7 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1582,52 +578,43 @@ - - - - - - - - - - - - + + + + + + + + + + + + + P8 + ko - - - - P8 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1645,51 +632,42 @@ - - - - - - - - - - - + + + + + + + + + + + + P9 + ko - - - - P9 - ko - - - - ko_f - ko_r - + + ko_f + ko_r nr + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1707,13 +685,13 @@ - - - - - - - + + + + + + + @@ -1721,13 +699,13 @@ X - - - - - - - + + + + + + + @@ -1735,13 +713,13 @@ S2 - - - - - - - + + + + + + + @@ -1749,13 +727,13 @@ S3 - - - - - - - + + + + + + + @@ -1763,8 +741,8 @@ Y - - - - + + + + diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props deleted file mode 100644 index d845eda..0000000 --- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props +++ /dev/null @@ -1,2 +0,0 @@ -// Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))] diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm deleted file mode 100644 index fea4690..0000000 --- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm +++ /dev/null @@ -1,295 +0,0 @@ -// File generated by automatic SBML-to-PRISM conversion -// Original SBML file: toggle.xml - -ctmc - -const int MAX_AMOUNT = 200; - -// Compartment size -const double default = 1.0; - -// Model parameters -const double kr_f = 0.5; // kr_f -const double kr_r = 1; // kr_r -const double ka_f = 0.0033; // ka_f -const double ka_r = 1; // ka_r -const double kc_f = 0.05; // kc_f -const double kc_r = 1; // kc_r -const double ko_f = 0.033; // ko_f -const double ko_r = 1; // ko_r -const double kao_f = 1; // kao_f -const double kao_r = 1; // kao_r -const double kmdiff_f = 1; // kmdiff_f -const double kmdiff_r = 0.01; // kmdiff_r -const double kd = 0.0075; // kd -const double kecd = 0.005; // kecd -const double nc = 2; // nc -const double nr = 30; // nr -const double ko = 0.05; // ko -const double kb = 0.0001; // kb -const double ng = 2; // ng -const double np = 10; // np -const double ka = 0.25; // ka -const double kecdiff = 1; // kecdiff - -// Species AA -const int AA_MAX = MAX_AMOUNT; -module AA - - AA : [0..AA_MAX] init 0; // Initial amount 0 - - -endmodule - -// Species B -const int B_MAX = MAX_AMOUNT; -module B - - B : [0..B_MAX] init 120; // Initial amount 120 - - -endmodule - -// Species Cout -const int Cout_MAX = MAX_AMOUNT; -module Cout - - Cout : [0..Cout_MAX] init 120; // Initial amount 120 - - // Degradation_Cout - [Degradation_Cout] Cout > 0 -> (Cout'=Cout-1); - // Production_P5 - [Production_P5] Cout <= Cout_MAX-10 -> (Cout'=Cout+10); - -endmodule - -// Species D -const int D_MAX = MAX_AMOUNT; -module D - - D : [0..D_MAX] init 0; // Initial amount 0 - - // Degradation_D - [Degradation_D] D > 0 -> (D'=D-1); - // Production_P1 - [Production_P1] D <= D_MAX-10 -> (D'=D+10); - -endmodule - -// Species EE -const int EE_MAX = MAX_AMOUNT; -module EE - - EE : [0..EE_MAX] init 0; // Initial amount 0 - - // Degradation_EE - [Degradation_EE] EE > 0 -> (EE'=EE-1); - // Production_P2 - [Production_P2] EE <= EE_MAX-10 -> (EE'=EE+10); - -endmodule - -// Species FF -const int FF_MAX = MAX_AMOUNT; -module FF - - FF : [0..FF_MAX] init 200; // Initial amount 200 - - // Degradation_FF - [Degradation_FF] FF > 0 -> (FF'=FF-1); - // Production_P8 - [Production_P8] FF <= FF_MAX-10 -> (FF'=FF+10); - // Production_P7 - [Production_P7] FF <= FF_MAX-10 -> (FF'=FF+10); - -endmodule - -// Species XX -const int XX_MAX = MAX_AMOUNT; -module XX - - XX : [0..XX_MAX] init 0; // Initial amount 0 - - // Degradation_XX - [Degradation_XX] XX > 0 -> (XX'=XX-1); - // Production_P1 - [Production_P1] XX <= XX_MAX-10 -> (XX'=XX+10); - // Production_P2 - [Production_P2] XX <= XX_MAX-10 -> (XX'=XX+10); - -endmodule - -// Species Y -const int Y_MAX = MAX_AMOUNT; -module Y - - Y : [0..Y_MAX] init 200; // Initial amount 200 - - // Degradation_Y - [Degradation_Y] Y > 0 -> (Y'=Y-1); - // Production_P5 - [Production_P5] Y <= Y_MAX-10 -> (Y'=Y+10); - // Production_P3 - [Production_P3] Y <= Y_MAX-10 -> (Y'=Y+10); - -endmodule - -// Species Z -const int Z_MAX = MAX_AMOUNT; -module Z - - Z : [0..Z_MAX] init 0; // Initial amount 0 - - // Degradation_Z - [Degradation_Z] Z > 0 -> (Z'=Z-1); - // Production_P4 - [Production_P4] Z <= Z_MAX-10 -> (Z'=Z+10); - // Production_P6 - [Production_P6] Z <= Z_MAX-10 -> (Z'=Z+10); - -endmodule - -// Species P8 -const int P8_MAX = MAX_AMOUNT; -module P8 - - P8 : [0..P8_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P5 -const int P5_MAX = MAX_AMOUNT; -module P5 - - P5 : [0..P5_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P4 -const int P4_MAX = MAX_AMOUNT; -module P4 - - P4 : [0..P4_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P7 -const int P7_MAX = MAX_AMOUNT; -module P7 - - P7 : [0..P7_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P6 -const int P6_MAX = MAX_AMOUNT; -module P6 - - P6 : [0..P6_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P1 -const int P1_MAX = MAX_AMOUNT; -module P1 - - P1 : [0..P1_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P3 -const int P3_MAX = MAX_AMOUNT; -module P3 - - P3 : [0..P3_MAX] init 2; // Initial amount 2 - - -endmodule - -// Species P2 -const int P2_MAX = MAX_AMOUNT; -module P2 - - P2 : [0..P2_MAX] init 2; // Initial amount 2 - - -endmodule - -// Reaction rates -module reaction_rates - - // Degradation_D: D -> - [Degradation_D] (kd*D) > 0 -> (kd*D) : true; - // Degradation_EE: EE -> - [Degradation_EE] (kd*EE) > 0 -> (kd*EE) : true; - // Degradation_FF: FF -> - [Degradation_FF] (kd*FF) > 0 -> (kd*FF) : true; - // Degradation_Cout: Cout -> - [Degradation_Cout] (kd*Cout) > 0 -> (kd*Cout) : true; - // Degradation_Y: Y -> - [Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true; - // Degradation_XX: XX -> - [Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true; - // Degradation_Z: Z -> - [Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true; - // Production_P8: -> FF - [Production_P8] (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*EE),nc)))) > 0 -> (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*EE),nc)))) : true; - // Production_P5: -> Y+Cout - [Production_P5] (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) : true; - // Production_P4: -> Z - [Production_P4] (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*FF),nc)))) > 0 -> (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*FF),nc)))) : true; - // Production_P7: -> FF - [Production_P7] (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*D),nc)))) : true; - // Production_P6: -> Z - [Production_P6] (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) : true; - // Production_P1: -> D+XX - [Production_P1] (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) : true; - // Production_P3: -> Y - [Production_P3] (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) : true; - // Production_P2: -> EE+XX - [Production_P2] (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) : true; - -endmodule - -// Reward structures (one per species) - -// Reward 1: AA -rewards "AA" true : AA; endrewards -// Reward 2: B -rewards "B" true : B; endrewards -// Reward 3: Cout -rewards "Cout" true : Cout; endrewards -// Reward 4: D -rewards "D" true : D; endrewards -// Reward 5: EE -rewards "EE" true : EE; endrewards -// Reward 6: FF -rewards "FF" true : FF; endrewards -// Reward 7: XX -rewards "XX" true : XX; endrewards -// Reward 8: Y -rewards "Y" true : Y; endrewards -// Reward 9: Z -rewards "Z" true : Z; endrewards -// Reward 10: P8 -rewards "P8" true : P8; endrewards -// Reward 11: P5 -rewards "P5" true : P5; endrewards -// Reward 12: P4 -rewards "P4" true : P4; endrewards -// Reward 13: P7 -rewards "P7" true : P7; endrewards -// Reward 14: P6 -rewards "P6" true : P6; endrewards -// Reward 15: P1 -rewards "P1" true : P1; endrewards -// Reward 16: P3 -rewards "P3" true : P3; endrewards -// Reward 17: P2 -rewards "P2" true : P2; endrewards diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml deleted file mode 100755 index 69fcc57..0000000 --- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml +++ /dev/null @@ -1,1137 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - D - - - - - - - - - - - - - kd - EE - - - - - - - - - - - - - kd - FF - - - - - - - - - - - - - kd - Cout - - - - - - - - - - - - - kd - Y - - - - - - - - - - - - - kd - XX - - - - - - - - - - - - - kd - Z - - - - - - - - - - - - - - - - - - - - - - - - - P8 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - EE - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - P5 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - Z - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P4 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - FF - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P7 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - D - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P6 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - Y - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - P1 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - AA - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P3 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - XX - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - - P2 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - B - - nc - - - - - - - - - - - - - - t - 5000 - - - - - - 0 - - - - - - 40 - - - - - - - - - - t - 10000 - - - - - - 0 - - - - - - 40 - - - - - - - - - - t - 15000 - - - - - - 0 - - - - - - 0 - - - - - - - - - - t - 20000 - - - - - - 0 - - - - - - 0 - - - - - - - diff --git a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.jani 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"initial-value": 2, + "name": "P7", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 120 + } + } + ] +} diff --git a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props index d845eda..b5f6aaa 100644 --- a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props +++ b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props @@ -1,2 +1,4 @@ // Probability that the toggle switch changes state erroneously within T time units. -"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))] +//"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))] + +P=? [ true U[0,50] (Y <= 50) ] diff --git a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml index 59265dc..9140703 100644 --- a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml +++ b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml @@ -1,790 +1,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + @@ -806,50 +24,50 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + F @@ -873,18 +91,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -894,11 +112,8 @@ - - - P8 - ko - + P8 + ko ko_f ko_r @@ -907,18 +122,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -936,18 +148,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -957,11 +169,8 @@ - - - P1 - ko - + P1 + ko ko_f ko_r @@ -970,18 +179,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -999,18 +205,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -1020,11 +226,8 @@ - - - P2 - ko - + P2 + ko ko_f ko_r @@ -1033,18 +236,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1062,17 +262,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1082,11 +282,8 @@ - - - P3 - ko - + P3 + ko ko_f ko_r @@ -1095,18 +292,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1124,17 +318,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1144,11 +338,8 @@ - - - P4 - ko - + P4 + ko ko_f ko_r @@ -1157,18 +348,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1186,18 +374,18 @@ - - - - - - - - - - - - + + + + + + + + + + + + @@ -1207,11 +395,8 @@ - - - P5 - ko - + P5 + ko ko_f ko_r @@ -1220,18 +405,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1249,17 +431,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1269,11 +451,8 @@ - - - P6 - ko - + P6 + ko ko_f ko_r @@ -1282,18 +461,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1311,17 +487,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -1331,11 +507,8 @@ - - - P7 - ko - + P7 + ko ko_f ko_r @@ -1344,18 +517,15 @@ + 1 - - 1 + - - - - ko_f - ko_r - - nr + + ko_f + ko_r + nr @@ -1373,13 +543,13 @@ - - - - - - - + + + + + + + @@ -1387,13 +557,13 @@ E - - - - - - - + + + + + + + @@ -1401,13 +571,13 @@ C - - - - - - - + + + + + + + @@ -1415,13 +585,13 @@ X - - - - - - 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"variables": [] + } + ], + "constants": [ + { + "name": "MAX_AMOUNT", + "type": "int", + "value": 100 + }, + { + "name": "Cell", + "type": "real", + "value": 1 + }, + { + "name": "kd", + "type": "real", + "value": 0.0075 + }, + { + "name": "kr_f", + "type": "real", + "value": 0.5 + }, + { + "name": "kr_r", + "type": "real", + "value": 1 + }, + { + "name": "ka_f", + "type": "real", + "value": 0.0033 + }, + { + "name": "ka_r", + "type": "real", + "value": 1 + }, + { + "name": "ko_f", + "type": "real", + "value": 0.033 + }, + { + "name": "ko_r", + "type": "real", + "value": 1 + }, + { + "name": "kao_f", + "type": "real", + "value": 1 + }, + { + "name": "kao_r", + "type": "real", + "value": 1 + }, + { + "name": "nc", + "type": "real", + "value": 2 + }, + { + "name": "nr", + "type": "real", + "value": 30 + }, + { + "name": "ko", + "type": "real", + "value": 0.05 + }, + { + "name": "kb", + "type": "real", + "value": 0.0001 + }, + { + "name": "ng", + "type": "real", + "value": 2 + }, + { + "name": "np", + "type": "real", + "value": 10 + }, + { + "name": "ka", + "type": "real", + "value": 0.25 + }, + { + "name": "CI_MAX", + "type": "int", + "value": 100 + }, + { + "name": "LacI_MAX", + "type": "int", + "value": 100 + }, + { + "name": "TetR_MAX", + "type": "int", + "value": 100 + }, + { + "name": "P0_MAX", + "type": "int", + "value": 100 + }, + { + "name": "P1_MAX", + "type": "int", + "value": 100 + }, + { + "name": "P2_MAX", + "type": "int", + "value": 100 + } + ], + "features": [ + "derived-operators" + ], + "jani-version": 1, + "name": "Repressilator", + "properties": [ + { + "expression": { + "fun": "values", + "op": "filter", + "states": { + "op": "initial" + }, + "values": { + "exp": { + "left": true, + "op": "U", + "right": { + "left": "CI", + "op": "≥", + "right": 12 + }, + "time-bounds": { + "lower": 0, + "lower-exclusive": false, + "upper": 50, + "upper-exclusive": false + } + }, + "op": "Pmin" + } + }, + "name": "1" + } + ], + "restrict-initial": { + "exp": true + }, + "system": { + "elements": [ + { + "automaton": "CI" + }, + { + "automaton": "LacI" + }, + { + "automaton": "TetR" + }, + { + "automaton": "P0" + }, + { + "automaton": "P1" + }, + { + "automaton": "P2" + }, + { + "automaton": "reaction_rates" + } + ], + "syncs": [ + { + "result": "Degradation_CI", + "synchronise": [ + "Degradation_CI", + null, + null, + null, + null, + null, + "Degradation_CI" + ] + }, + { + "result": "Degradation_LacI", + "synchronise": [ + null, + "Degradation_LacI", + null, + null, + null, + null, + "Degradation_LacI" + ] + }, + { + "result": "Degradation_TetR", + "synchronise": [ + null, + null, + "Degradation_TetR", + null, + null, + null, + "Degradation_TetR" + ] + }, + { + "result": "Production_P0", + "synchronise": [ + null, + "Production_P0", + null, + null, + null, + null, + "Production_P0" + ] + }, + { + "result": "Production_P1", + "synchronise": [ + null, + null, + "Production_P1", + null, + null, + null, + "Production_P1" + ] + }, + { + "result": "Production_P2", + "synchronise": [ + "Production_P2", + null, + null, + null, + null, + null, + "Production_P2" + ] + } + ] + }, + "type": "ctmc", + "variables": [ + { + "initial-value": 0, + "name": "rewardmodel_CI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_LacI", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_TetR", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P0", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P1", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "rewardmodel_P2", + "transient": true, + "type": "real" + }, + { + "initial-value": 0, + "name": "CI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "LacI", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 0, + "name": "TetR", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "P0", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "P1", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + }, + { + "initial-value": 2, + "name": "P2", + "type": { + "base": "int", + "kind": "bounded", + "lower-bound": 0, + "upper-bound": 100 + } + } + ] +} diff --git a/GeneticCircuits/Repressilator/Default/Repressilator.props b/GeneticCircuits/Repressilator/Default/Repressilator.props new file mode 100644 index 0000000..9a5571b --- /dev/null +++ b/GeneticCircuits/Repressilator/Default/Repressilator.props @@ -0,0 +1 @@ +P=? [ true U[0,50] (CI >= 12) ] diff --git a/GeneticCircuits/Repressilator/Default/Repressilator.xml b/GeneticCircuits/Repressilator/Default/Repressilator.xml index 3d179f9..7b71588 100755 --- a/GeneticCircuits/Repressilator/Default/Repressilator.xml +++ b/GeneticCircuits/Repressilator/Default/Repressilator.xml @@ -1,8 +1,8 @@ - - - - + + + + @@ -17,8 +17,8 @@ - - + + @@ -34,39 +34,39 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + St @@ -125,14 +125,14 @@ - - - - - - - - + + + + + + + + @@ -140,13 +140,13 @@ CI - - - - - - - + + + + + + + @@ -154,13 +154,13 @@ LacI - - - - - - - + + + + + + + @@ -168,17 +168,17 @@ TetR - - - - - - - - - - - + + + + + + + + + + + @@ -221,17 +221,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -274,17 +274,17 @@ - - - - - - - - - - - + + + + + + + + + + + @@ -327,140 +327,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + diff --git a/GeneticCircuits/Repressilator/Default/results.txt b/GeneticCircuits/Repressilator/Default/results.txt new file mode 100644 index 0000000..86ea27e --- /dev/null +++ b/GeneticCircuits/Repressilator/Default/results.txt @@ -0,0 +1,2 @@ +0.3802594776197713 +0.38025948379759894 diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props deleted file mode 100644 index 87ad135..0000000 --- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props +++ /dev/null @@ -1,4 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: Toggle_Switch.xml -// @GeneticLogicLab - diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm deleted file mode 100644 index e913ff0..0000000 --- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm +++ /dev/null @@ -1,199 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: Toggle_Switch.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 0.0075; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double topModell_Part2_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModell_Part2_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModell_Part2_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModell_Part2_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModell_Part2_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModell_Part2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModell_Part2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModell_Part2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModell_Part2_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModell_Part2_module_sub__nr = 30.0; // Initial RNAP count -const double topModell_Part2_module_sub__ko = 0.05; // Open complex production rate -const double topModell_Part2_module_sub__kb = 1.0E-4; // Basal production rate -const double topModell_Part2_module_sub__ng = 2.0; // Initial promoter count -const double topModell_Part2_module_sub__np = 10.0; // Stoichiometry of production -const double topModell_Part2_module_sub__ka = 0.25; // Activated production rate -const double topModell_Part1_module_sub__kr_f = 0.5; // Forward repression binding rate -const double topModell_Part1_module_sub__kr_r = 1.0; // Reverse repression binding rate -const double topModell_Part1_module_sub__ka_f = 0.0033; // Forward activation binding rate -const double topModell_Part1_module_sub__ka_r = 1.0; // Reverse activation binding rate -const double topModell_Part1_module_sub__ko_f = 0.033; // Forward RNAP binding rate -const double topModell_Part1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate -const double topModell_Part1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate -const double topModell_Part1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate -const double topModell_Part1_module_sub__nc = 2.0; // Stoichiometry of binding -const double topModell_Part1_module_sub__nr = 30.0; // Initial RNAP count -const double topModell_Part1_module_sub__ko = 0.05; // Open complex production rate -const double topModell_Part1_module_sub__kb = 1.0E-4; // Basal production rate -const double topModell_Part1_module_sub__ng = 2.0; // Initial promoter count -const double topModell_Part1_module_sub__np = 10.0; // Stoichiometry of production -const double topModell_Part1_module_sub__ka = 0.25; // Activated production rate - -// Species IPTG -module IPTG - - IPTG : int init 0; - - // Complex_IPTG_LacI_protein - [Complex_IPTG_LacI_protein] IPTG > 0 -> (IPTG' = IPTG - 2); - -endmodule - -// Species aTc -module aTc - - aTc : int init 0; - - // Complex_aTc_TetR_protein - [Complex_aTc_TetR_protein] aTc > 0 -> (aTc' = aTc - 2); - -endmodule - -// Species YFP_protein -module YFP_protein - - YFP_protein : int init 0; - - // Degradation_YFP_protein - [Degradation_YFP_protein] YFP_protein > 0 -> (YFP_protein' = YFP_protein - 1); - // R_abstracted_production_topModell_Part2_module_sub__Part2_fc - [R_abstracted_production_topModell_Part2_module_sub__Part2_fc] YFP_protein > 0 -> (YFP_protein' = YFP_protein + 10); - -endmodule - -// Species aTc_TetR_protein -module aTc_TetR_protein - - aTc_TetR_protein : int init 0; - - // Degradation_aTc_TetR_protein - [Degradation_aTc_TetR_protein] aTc_TetR_protein > 0 -> (aTc_TetR_protein' = aTc_TetR_protein - 1); - // Complex_aTc_TetR_protein - [Complex_aTc_TetR_protein] aTc_TetR_protein > 0 -> (aTc_TetR_protein' = aTc_TetR_protein + 1); - -endmodule - -// Species LacI_protein -module LacI_protein - - LacI_protein : int init 0; - - // Degradation_LacI_protein - [Degradation_LacI_protein] LacI_protein > 0 -> (LacI_protein' = LacI_protein - 1); - // R_abstracted_production_topModell_Part2_module_sub__Part2_fc - [R_abstracted_production_topModell_Part2_module_sub__Part2_fc] LacI_protein > 0 -> (LacI_protein' = LacI_protein + 10); - // Complex_IPTG_LacI_protein - [Complex_IPTG_LacI_protein] LacI_protein > 0 -> (LacI_protein' = LacI_protein - 2); - -endmodule - -// Species IPTG_LacI_protein -module IPTG_LacI_protein - - IPTG_LacI_protein : int init 0; - - // Degradation_IPTG_LacI_protein - [Degradation_IPTG_LacI_protein] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein' = IPTG_LacI_protein - 1); - // Complex_IPTG_LacI_protein - [Complex_IPTG_LacI_protein] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein' = IPTG_LacI_protein + 1); - -endmodule - -// Species TetR_protein -module TetR_protein - - TetR_protein : int init 60; - - // Degradation_TetR_protein - [Degradation_TetR_protein] TetR_protein > 0 -> (TetR_protein' = TetR_protein - 1); - // R_abstracted_production_topModell_Part1_module_sub__Part1_fc - [R_abstracted_production_topModell_Part1_module_sub__Part1_fc] TetR_protein > 0 -> (TetR_protein' = TetR_protein + 10); - // Complex_aTc_TetR_protein - [Complex_aTc_TetR_protein] TetR_protein > 0 -> (TetR_protein' = TetR_protein - 2); - -endmodule - -// Species topModell_Part2_module_sub__Part2_fc -module topModell_Part2_module_sub__Part2_fc - - topModell_Part2_module_sub__Part2_fc : int init 2; - - -endmodule - -// Species topModell_Part1_module_sub__Part1_fc -module topModell_Part1_module_sub__Part1_fc - - topModell_Part1_module_sub__Part1_fc : int init 2; - - -endmodule - -// Reaction rates -module reaction_rates - - // Degradation_aTc_TetR_protein: -> aTc_TetR_protein -> - [Degradation_aTc_TetR_protein] (kd * aTc_TetR_protein) > 0 -> (kd * aTc_TetR_protein) : true; - - // Degradation_YFP_protein: -> YFP_protein -> - [Degradation_YFP_protein] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true; - - // Degradation_LacI_protein: -> LacI_protein -> - [Degradation_LacI_protein] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true; - - // Degradation_IPTG_LacI_protein: -> IPTG_LacI_protein -> - [Degradation_IPTG_LacI_protein] (kd * IPTG_LacI_protein) > 0 -> (kd * IPTG_LacI_protein) : true; - - // Degradation_TetR_protein: -> TetR_protein -> - [Degradation_TetR_protein] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true; - - // R_abstracted_production_topModell_Part1_module_sub__Part1_fc: -> -> -TetR_protein - [R_abstracted_production_topModell_Part1_module_sub__Part1_fc] (((ko__topModell_Part1_module_sub__Part1_fc * ng__topModell_Part1_module_sub__Part1_fc) * (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) / ((1 + (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) + pow((Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc * LacI_protein) , nc__LacI_protein_topModell_Part1_module_sub__Part1_fc))) > 0 -> (((ko__topModell_Part1_module_sub__Part1_fc * ng__topModell_Part1_module_sub__Part1_fc) * (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) / ((1 + (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) + pow((Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc * LacI_protein) , nc__LacI_protein_topModell_Part1_module_sub__Part1_fc))) : true; - - // R_abstracted_production_topModell_Part2_module_sub__Part2_fc: -> -> -YFP_protein + -LacI_protein - [R_abstracted_production_topModell_Part2_module_sub__Part2_fc] (((ko__topModell_Part2_module_sub__Part2_fc * ng__topModell_Part2_module_sub__Part2_fc) * (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) / ((1 + (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) + pow((Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc * TetR_protein) , nc__TetR_protein_topModell_Part2_module_sub__Part2_fc))) > 0 -> (((ko__topModell_Part2_module_sub__Part2_fc * ng__topModell_Part2_module_sub__Part2_fc) * (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) / ((1 + (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) + pow((Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc * TetR_protein) , nc__TetR_protein_topModell_Part2_module_sub__Part2_fc))) : true; - - // Complex_aTc_TetR_protein: -> aTc + TetR_protein -> aTc_TetR_protein - [Complex_aTc_TetR_protein] ((((kf_c * pow(Kc , ((nc__aTc_aTc_TetR_protein + nc__TetR_protein_aTc_TetR_protein) - 2))) * pow(aTc , nc__aTc_aTc_TetR_protein)) * pow(TetR_protein , nc__TetR_protein_aTc_TetR_protein)) - (kr_c * aTc_TetR_protein)) > 0 -> ((((kf_c * pow(Kc , ((nc__aTc_aTc_TetR_protein + nc__TetR_protein_aTc_TetR_protein) - 2))) * pow(aTc , nc__aTc_aTc_TetR_protein)) * pow(TetR_protein , nc__TetR_protein_aTc_TetR_protein)) - (kr_c * aTc_TetR_protein)) : true; - - // Complex_IPTG_LacI_protein: -> IPTG + LacI_protein -> IPTG_LacI_protein - [Complex_IPTG_LacI_protein] ((((kf_c * pow(Kc , ((nc__IPTG_IPTG_LacI_protein + nc__LacI_protein_IPTG_LacI_protein) - 2))) * pow(IPTG , nc__IPTG_IPTG_LacI_protein)) * pow(LacI_protein , nc__LacI_protein_IPTG_LacI_protein)) - (kr_c * IPTG_LacI_protein)) > 0 -> ((((kf_c * pow(Kc , ((nc__IPTG_IPTG_LacI_protein + nc__LacI_protein_IPTG_LacI_protein) - 2))) * pow(IPTG , nc__IPTG_IPTG_LacI_protein)) * pow(LacI_protein , nc__LacI_protein_IPTG_LacI_protein)) - (kr_c * IPTG_LacI_protein)) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: IPTG -rewards "IPTG" true : IPTG; endrewards -// Reward 2: aTc -rewards "aTc" true : aTc; endrewards -// Reward 3: YFP_protein -rewards "YFP_protein" true : YFP_protein; endrewards -// Reward 4: aTc_TetR_protein -rewards "aTc_TetR_protein" true : aTc_TetR_protein; endrewards -// Reward 5: LacI_protein -rewards "LacI_protein" true : LacI_protein; endrewards -// Reward 6: IPTG_LacI_protein -rewards "IPTG_LacI_protein" true : IPTG_LacI_protein; endrewards -// Reward 7: TetR_protein -rewards "TetR_protein" true : TetR_protein; endrewards -// Reward 8: topModell_Part2_module_sub__Part2_fc -rewards "topModell_Part2_module_sub__Part2_fc" true : topModell_Part2_module_sub__Part2_fc; endrewards -// Reward 9: topModell_Part1_module_sub__Part1_fc -rewards "topModell_Part1_module_sub__Part1_fc" true : topModell_Part1_module_sub__Part1_fc; endrewards diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml deleted file mode 100644 index 4b3cc68..0000000 --- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml +++ /dev/null @@ -1,1186 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - aTc_TetR_protein - - - - - - - - - - - - - - - - kd - YFP_protein - - - - - - - - - - - - - - - - kd - LacI_protein - - - - - - - - - - - - - - - - kd - IPTG_LacI_protein - - - - - - - - - - - - - - - - kd - TetR_protein - - - - - - - - - - - - - - - - - - - - - - - ko__topModell_Part1_module_sub__Part1_fc - ng__topModell_Part1_module_sub__Part1_fc - - - - Ko__topModell_Part1_module_sub__Part1_fc - RNAP - - - - - - - 1 - - - Ko__topModell_Part1_module_sub__Part1_fc - RNAP - - - - - - - Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc - LacI_protein - - nc__LacI_protein_topModell_Part1_module_sub__Part1_fc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ko__topModell_Part2_module_sub__Part2_fc - ng__topModell_Part2_module_sub__Part2_fc - - - - Ko__topModell_Part2_module_sub__Part2_fc - RNAP - - - - - - - 1 - - - Ko__topModell_Part2_module_sub__Part2_fc - RNAP - - - - - - - Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc - TetR_protein - - nc__TetR_protein_topModell_Part2_module_sub__Part2_fc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kf_c - - - Kc - - - - - nc__aTc_aTc_TetR_protein - nc__TetR_protein_aTc_TetR_protein - - 2 - - - - - - aTc - nc__aTc_aTc_TetR_protein - - - - - TetR_protein - nc__TetR_protein_aTc_TetR_protein - - - - - kr_c - aTc_TetR_protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kf_c - - - Kc - - - - - nc__IPTG_IPTG_LacI_protein - nc__LacI_protein_IPTG_LacI_protein - - 2 - - - - - - IPTG - nc__IPTG_IPTG_LacI_protein - - - - - LacI_protein - nc__LacI_protein_IPTG_LacI_protein - - - - - kr_c - IPTG_LacI_protein - - - - - - - - - - - - - - - - - - - - - - - 2000 - - - - - - 60 - - - - - - - - - - - - - 4000 - - - - - - 0 - - - - - - - - - - - - - 6000 - - - - - - 60 - - - - - - - - - - - - - 8000 - - - - - - 0 - - - - - - - diff --git a/GeneticCircuits/Toggle_Switch/Default/jsbml.log b/GeneticCircuits/Toggle_Switch/Default/jsbml.log deleted file mode 100644 index d568ccc..0000000 --- a/GeneticCircuits/Toggle_Switch/Default/jsbml.log +++ /dev/null @@ -1,130 +0,0 @@ -2023-02-02 12:06:16,124 ERROR o.s.j.x.p.SBMLCoreParser [main] Property substanceUnits is not defined in model for Level 2 and Version 2. -2023-02-02 12:06:16,125 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = substanceUnits, value 'mole' , element name = model -2023-02-02 12:06:16,126 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'substanceUnits' on the element model. Please check the specification for SBML. -2023-02-02 12:06:16,127 ERROR o.s.j.x.p.SBMLCoreParser [main] Property volumeUnits is not defined in model for Level 2 and Version 2. -2023-02-02 12:06:16,128 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = volumeUnits, value 'litre' , element name = model -2023-02-02 12:06:16,128 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'volumeUnits' on the element model. Please check the specification for SBML. -2023-02-02 12:06:16,129 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,171 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,172 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,173 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,175 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,176 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,177 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,178 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,221 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,222 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost -2023-02-02 12:06:16,228 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,229 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,229 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,230 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,230 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,231 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,235 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,236 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,236 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,236 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,237 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,237 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,237 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,238 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,239 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,239 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,240 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,240 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,241 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,241 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,241 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,242 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,242 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,242 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,243 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,243 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,243 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,244 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,244 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,244 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,244 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,245 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,245 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,245 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,246 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,246 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,246 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,246 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,247 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,247 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,247 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,249 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,250 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,250 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,250 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,251 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,251 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,251 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,252 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,252 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,252 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,254 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,255 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,255 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,255 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,255 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,256 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,256 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,256 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,256 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,256 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,257 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,257 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,257 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,258 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,259 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2. -2023-02-02 12:06:16,259 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:06:16,259 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:06:16,259 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,259 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,260 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,260 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,260 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,260 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,261 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2. -2023-02-02 12:06:16,261 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:06:16,261 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:06:16,262 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:06:16,263 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2. -2023-02-02 12:06:16,263 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:06:16,263 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:06:16,264 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,264 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:06:16,264 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,265 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,265 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:06:16,265 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,266 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2. -2023-02-02 12:06:16,266 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:06:16,266 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:06:16,267 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,267 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:06:16,267 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,267 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,267 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:06:16,267 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,268 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2. -2023-02-02 12:06:16,268 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:06:16,268 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:06:16,269 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,269 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:06:16,269 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,269 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,269 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:06:16,269 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,270 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2. -2023-02-02 12:06:16,270 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:06:16,270 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:06:16,271 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,271 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:06:16,271 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:06:16,271 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2. -2023-02-02 12:06:16,271 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:06:16,271 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props deleted file mode 100644 index dab0e7a..0000000 --- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props +++ /dev/null @@ -1,4 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: Toggle_Switch_RBA.xml -// @GeneticLogicLab - diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm deleted file mode 100644 index 2119e38..0000000 --- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm +++ /dev/null @@ -1,183 +0,0 @@ -// File generated by SBML-to-PRISM converter -// Original file: Toggle_Switch_RBA.xml -// @GeneticLogicLab - -ctmc - -// Compartment size -const double Cell = 1.0; - -// Model parameters -const double kd = 0.0075; // Degradation rate -const double kc_f = 0.05; // Forward complex formation rate -const double kc_r = 1.0; // Reverse complex formation rate -const double nc = 2.0; // Stoichiometry of binding -const double kr_f = 0.5; // Forward repression binding rate -const double kr_r = 1.0; // Reverse repression binding rate -const double ka_f = 0.0033; // Forward activation binding rate -const double ka_r = 1.0; // Reverse activation binding rate -const double ko_f = 0.033; // Forward RNAP binding rate -const double ko_r = 1.0; // Reverse RNAP binding rate -const double kao_f = 1.0; // Forward activated RNAP binding rate -const double kao_r = 1.0; // Reverse activated RNAP binding rate -const double nr = 30.0; // Initial RNAP count -const double ko = 0.05; // Open complex production rate -const double kb = 1.0E-4; // Basal production rate -const double ng = 2.0; // Initial promoter count -const double np = 10.0; // Stoichiometry of production -const double ka = 0.25; // Activated production rate - -// Species P1 -module P1 - - P1 : int init 2; - - -endmodule - -// Species IPTG -module IPTG - - IPTG : int init 0; - - // Complex_C1 - [Complex_C1] IPTG > 0 -> (IPTG' = IPTG - 1); - -endmodule - -// Species aTc -module aTc - - aTc : int init 0; - - // Complex_C2 - [Complex_C2] aTc > 0 -> (aTc' = aTc - 1); - -endmodule - -// Species TetR -module TetR - - TetR : int init 0; - - // Degradation_TetR - [Degradation_TetR] TetR > 0 -> (TetR' = TetR - 1); - // Complex_C2 - [Complex_C2] TetR > 0 -> (TetR' = TetR - 1); - // Production_P1 - [Production_P1] TetR > 0 -> (TetR' = TetR + 10); - -endmodule - -// Species GFP -module GFP - - GFP : int init 0; - - // Degradation_GFP - [Degradation_GFP] GFP > 0 -> (GFP' = GFP - 1); - // Production_P1 - [Production_P1] GFP > 0 -> (GFP' = GFP + 10); - -endmodule - -// Species P2 -module P2 - - P2 : int init 2; - - -endmodule - -// Species C1 -module C1 - - C1 : int init 0; - - // Degradation_C1 - [Degradation_C1] C1 > 0 -> (C1' = C1 - 1); - // Complex_C1 - [Complex_C1] C1 > 0 -> (C1' = C1 + 1); - -endmodule - -// Species C2 -module C2 - - C2 : int init 0; - - // Degradation_C2 - [Degradation_C2] C2 > 0 -> (C2' = C2 - 1); - // Complex_C2 - [Complex_C2] C2 > 0 -> (C2' = C2 + 1); - -endmodule - -// Species LacI -module LacI - - LacI : int init 0; - - // Degradation_LacI - [Degradation_LacI] LacI > 0 -> (LacI' = LacI - 1); - // Complex_C1 - [Complex_C1] LacI > 0 -> (LacI' = LacI - 1); - // Production_P2 - [Production_P2] LacI > 0 -> (LacI' = LacI + 10); - -endmodule - -// Reaction rates -module reaction_rates - - // Degradation_TetR: -> TetR -> - [Degradation_TetR] (kd * TetR) > 0 -> (kd * TetR) : true; - - // Degradation_GFP: -> GFP -> - [Degradation_GFP] (kd * GFP) > 0 -> (kd * GFP) : true; - - // Degradation_C2: -> C2 -> - [Degradation_C2] (kd * C2) > 0 -> (kd * C2) : true; - - // Degradation_LacI: -> LacI -> - [Degradation_LacI] (kd * LacI) > 0 -> (kd * LacI) : true; - - // Degradation_C1: -> C1 -> - [Degradation_C1] (kd * C1) > 0 -> (kd * C1) : true; - - // Complex_C1: -> IPTG + LacI -> C1 - [Complex_C1] (((kc_f * pow(IPTG , nc_IPTG)) * pow(LacI , nc_LacI)) - (kc_r * C1)) > 0 -> (((kc_f * pow(IPTG , nc_IPTG)) * pow(LacI , nc_LacI)) - (kc_r * C1)) : true; - - // Complex_C2: -> aTc + TetR -> C2 - [Complex_C2] (((kc_f * pow(aTc , nc_aTc)) * pow(TetR , nc_TetR)) - (kc_r * C2)) > 0 -> (((kc_f * pow(aTc , nc_aTc)) * pow(TetR , nc_TetR)) - (kc_r * C2)) : true; - - // Production_P1: -> -> -GFP + -TetR - [Production_P1] (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) > 0 -> (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) : true; - - // Production_P2: -> -> -LacI - [Production_P2] (((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) > 0 -> (((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) : true; - -endmodule - -// Reward structures (one per species) -// Reward 1: P1 -rewards "P1" true : P1; endrewards -// Reward 2: IPTG -rewards "IPTG" true : IPTG; endrewards -// Reward 3: aTc -rewards "aTc" true : aTc; endrewards -// Reward 4: TetR -rewards "TetR" true : TetR; endrewards -// Reward 5: GFP -rewards "GFP" true : GFP; endrewards -// Reward 6: P2 -rewards "P2" true : P2; endrewards -// Reward 7: C1 -rewards "C1" true : C1; endrewards -// Reward 8: C2 -rewards "C2" true : C2; endrewards -// Reward 9: LacI -rewards "LacI" true : LacI; endrewards diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml deleted file mode 100644 index 73a0998..0000000 --- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml +++ /dev/null @@ -1,798 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - kd - TetR - - - - - - - - - - - - - kd - GFP - - - - - - - - - - - - - kd - C2 - - - - - - - - - - - - - kd - LacI - - - - - - - - - - - - - kd - C1 - - - - - - - - - - - - - - - - - - - - - kc_f - - - IPTG - nc_IPTG - - - - - LacI - nc_LacI - - - - - kc_r - C1 - - - - - - - - - - - - - - - - - - - - - - - - - - kc_f - - - aTc - nc_aTc - - - - - TetR - nc_TetR - - - - - kc_r - C2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - P1 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - LacI - - nc - - - - - - - - - - - - - - - - - - - - - - - - - - - P2 - ko - - ko_f - - ko_r - - nr - - - - - - 1 - - - - - ko_f - ko_r - - nr - - - - - - - - - kr_f - kr_r - - TetR - - nc - - - - - - - - - - - - - - t - 500 - - - - - - - 60 - - - - - - - - - - t - 1500 - - - - - - - 0 - - - - - - - - - - t - 2000 - - - - - - - 60 - - - - - - - - - - t - 3000 - - - - - - - 0 - - - - - - - diff --git a/GeneticCircuits/Toggle_Switch/RBA/jsbml.log b/GeneticCircuits/Toggle_Switch/RBA/jsbml.log deleted file mode 100644 index 8bda126..0000000 --- a/GeneticCircuits/Toggle_Switch/RBA/jsbml.log +++ /dev/null @@ -1,107 +0,0 @@ -2023-02-02 12:08:21,958 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,960 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,960 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,962 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,963 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,963 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,966 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,966 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,966 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,967 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,967 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,967 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,968 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,968 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,968 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,969 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,969 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,969 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,970 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,970 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,970 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,971 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,971 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,971 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,972 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,972 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,972 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,973 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,973 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,973 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,974 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,974 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,974 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,974 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,974 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,975 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,975 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,975 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,975 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,976 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,976 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,976 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,977 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:08:21,977 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,977 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,978 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,978 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,978 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,978 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,979 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,979 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,979 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,979 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,979 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,980 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,981 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized. -2023-02-02 12:08:21,981 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,981 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,981 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,982 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,982 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,982 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,983 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,983 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,983 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,984 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1. -2023-02-02 12:08:21,985 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction -2023-02-02 12:08:21,985 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML. -2023-02-02 12:08:21,985 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1. -2023-02-02 12:08:21,985 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference -2023-02-02 12:08:21,985 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML. -2023-02-02 12:08:21,987 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1. -2023-02-02 12:08:21,987 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:08:21,987 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:08:21,988 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,988 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:08:21,988 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,988 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,988 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:08:21,988 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,989 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1. -2023-02-02 12:08:21,989 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:08:21,989 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:08:21,990 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,990 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:08:21,990 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,990 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,990 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:08:21,991 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,991 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1. -2023-02-02 12:08:21,991 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:08:21,991 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:08:21,992 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,992 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:08:21,992 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,992 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,992 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:08:21,992 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,993 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1. -2023-02-02 12:08:21,993 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event -2023-02-02 12:08:21,994 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML. -2023-02-02 12:08:21,994 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,994 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger -2023-02-02 12:08:21,994 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML. -2023-02-02 12:08:21,995 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1. -2023-02-02 12:08:21,995 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger -2023-02-02 12:08:21,995 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML. diff --git a/GeneticCircuits/Toggle_Switch/README.md b/GeneticCircuits/Toggle_Switch/README.md deleted file mode 100644 index 294a1e4..0000000 --- a/GeneticCircuits/Toggle_Switch/README.md +++ /dev/null @@ -1,7 +0,0 @@ -### Toggle Switch - -The toggle switch is a state holding gate and consists of two promoters each followed by a coding sequence. Each promoter is repressed by the protein transcribed by the other promoter [1]. - -![Figure7](../../Media/ToggleSwitch.png) - -1. Gardner, T. S.; Cantor, C. R.; Collins, J. J. Construction of a Genetic Toggle Switch in Escherichia Coli. Nature 2000, 403 (6767), 339–342. https://doi.org/10.1038/35002131. diff --git a/ParameterExploration/DoubleInv.props b/ParameterExploration/DoubleInv.props new file mode 100644 index 0000000..2f4c03b --- /dev/null +++ b/ParameterExploration/DoubleInv.props @@ -0,0 +1,2 @@ +// mScarlet count exceeded 10 molecules during the interval [1000, 2100] +P=?[F [1000, 2100] (mScarlet >= 10)] diff --git a/ParameterExploration/DoubleInv.sm b/ParameterExploration/DoubleInv.sm new file mode 100644 index 0000000..ab0a975 --- /dev/null +++ b/ParameterExploration/DoubleInv.sm @@ -0,0 +1,163 @@ +// File generated by SBML-to-PRISM converter +// Original file: DoubleInv.xml +// @GeneticLogicLab + +ctmc + +// Compartment size +const double Cell = 1.0; + +// Model parameters +const double kr_f = 0.5; // Forward repression binding rate +const double kr_r = 1.0; // Reverse repression binding rate +const double ka_f = 0.0033; // Forward activation binding rate +const double ka_r = 1.0; // Reverse activation binding rate +const double ko_f = 0.033; // Forward RNAP binding rate +const double ko_r = 1.0; // Reverse RNAP binding rate +const double kao_f = 1.0; // Forward activated RNAP binding rate +const double kao_r = 1.0; // Reverse activated RNAP binding rate +const double nc = 2.0; // Stoichiometry of binding +const double nr = 30.0; // Initial RNAP count +const double ko = 0.05; // Open complex production rate +const double kb = 1.0E-4; // Basal production rate +const double ng = 2.0; // Initial promoter count +const double np = 10.0; // Stoichiometry of production +const double ka = 0.25; // Activated production rate +const double kc_f = 0.05; // Forward complex formation rate +const double kc_r = 1.0; // Reverse complex formation rate + +const double kd_IPTGLacI = 0.0075; // Degradation rate +const double kd_LacI = 0.0075; // +const double kd_TetR = 0.0075; // +const double kd_mScarlet = 0.0075; // + +// Species LacI +module LacI + + LacI : int init 67; + + // Production_P2 + [Production_P2] LacI >= 0 -> (LacI' = LacI + 10); + // Complex_IPTGLacI + [Complex_IPTGLacI] IPTG > 1 & LacI > 1 -> (LacI' = LacI - 2); + // Degradation_LacI + [Degradation_LacI] LacI > 0 -> (LacI' = LacI - 1); + +endmodule + +// Species TetR +module TetR + + TetR : int init 0; + + // Production_P0 + [Production_P0] TetR >= 0 -> (TetR' = TetR + 10); + // Degradation_TetR + [Degradation_TetR] TetR > 0 -> (TetR' = TetR - 1); + +endmodule + +// Species mScarlet +module mScarlet + + mScarlet : int init 69; + + // Production_P1 + [Production_P1] mScarlet >= 0 -> (mScarlet' = mScarlet + 10); + // Degradation_mScarlet + [Degradation_mScarlet] mScarlet > 0 -> (mScarlet' = mScarlet - 1); + +endmodule + +// Species P0 +module P0 + + P0 : int init 2; + + +endmodule + +// Species P1 +module P1 + + P1 : int init 2; + + +endmodule + +// Species P2 +module P2 + + P2 : int init 2; + + +endmodule + +// Species IPTG +module IPTG + + IPTG : int init 60; + + // Complex_IPTGLacI + [Complex_IPTGLacI] IPTG > 1 & LacI > 1 -> (IPTG' = IPTG - 2); + +endmodule + +// Species IPTGLacI +module IPTGLacI + + IPTGLacI : int init 0; + + // Complex_IPTGLacI + [Complex_IPTGLacI] IPTG > 1 & LacI > 1 -> (IPTGLacI' = IPTGLacI + 1); + // Degradation_IPTGLacI + [Degradation_IPTGLacI] IPTGLacI > 0 -> (IPTGLacI' = IPTGLacI - 1); + +endmodule + +// Reaction rates +module reaction_rates + + // Production_P0: -> 10 TetR + [Production_P0] (((((P0 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) > 0 -> (((((P0 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) : true; + + // Production_P1: -> 10 mScarlet + [Production_P1] (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) > 0 -> (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) : true; + + // Production_P2: -> 10 LacI + [Production_P2] (((((P2 * ko) * ko_f) / ko_r) * nr) / (1 + ((ko_f / ko_r) * nr))) > 0 -> (((((P2 * ko) * ko_f) / ko_r) * nr) / (1 + ((ko_f / ko_r) * nr))) : true; + + // Complex_IPTGLacI: 2 IPTG + 2 LacI -> IPTGLacI + [Complex_IPTGLacI] (((kc_f * pow(IPTG , nc)) * pow(LacI , nc)) - (kc_r * IPTGLacI)) > 0 -> (((kc_f * pow(IPTG , nc)) * pow(LacI , nc)) - (kc_r * IPTGLacI)) : true; + + // Degradation_TetR: TetR -> + [Degradation_TetR] (kd_TetR * TetR) > 0 -> (kd_TetR * TetR) : true; + + // Degradation_LacI: LacI -> + [Degradation_LacI] (kd_LacI * LacI) > 0 -> (kd_LacI * LacI) : true; + + // Degradation_IPTGLacI: IPTGLacI -> + [Degradation_IPTGLacI] (kd_IPTGLacI * IPTGLacI) > 0 -> (kd_IPTGLacI * IPTGLacI) : true; + + // Degradation_mScarlet: mScarlet -> + [Degradation_mScarlet] (kd_mScarlet * mScarlet) > 0 -> (kd_mScarlet * mScarlet) : true; + +endmodule + +// Reward structures (one per species) +// Reward 1: LacI +rewards "LacI" true : LacI; endrewards +// Reward 2: TetR +rewards "TetR" true : TetR; endrewards +// Reward 3: mScarlet +rewards "mScarlet" true : mScarlet; endrewards +// Reward 4: P0 +rewards "P0" true : P0; endrewards +// Reward 5: P1 +rewards "P1" true : P1; endrewards +// Reward 6: P2 +rewards "P2" true : P2; endrewards +// Reward 7: IPTG +rewards "IPTG" true : IPTG; endrewards +// Reward 8: IPTGLacI +rewards "IPTGLacI" true : IPTGLacI; endrewards