Matlab program for the automatic generation of dynamical qualitative models from reaction networks.
The source code can be run with octave instead by using the option (OPTION=octave)
For instance:
make OPTION=octave
The inputs of the tool are specified in the following files located in the folder "case_studies/model/input_files" (where 'model' denotes the name of the model, either "Fig2_prozone242000", "Fig3_prozone212000", "Fig5a_unary_vs_binary200", or "Fig5b_unary_vs_binary700"):
- init_cond.txt: initial conditions of the model;
- reaction_rates.txt: the kinetic rates of the reactions;
- nb_sampl_interv.txt: the number of sampling intervals;
- model_reactions.txt: the reactions of the model;
- model_reactions_alphabet.txt: the alphabet of the model
- mass_invar.txt: a mass invariant of the model.
The following command:
- make
removes any output file, compile each model and translate all dot into pdf. The generated results (both .dot and .pdf files) are stored in the folder "case_studies/model/output_files" where "model" denotes the name of the model (here either "Fig2_prozone242000", "Fig3_prozone212000", "Fig5a_unary_vs_binary200", or "Fig5b_unary_vs_binary700").
It is also possible to decompose the computation of this script stepwise.
The following command removes any existing output:
- make clean
The following commands generate the results from the inputs:
- make Fig2_prozone242000: to generate the results for the prozone case study, with initial state 242000
- make Fig3_prozone212000: to generate the results for the prozone case study, with initial state 212000
- make Fig5a_unary_vs_binary200: to generate the results for the unary vs binary case study with initial state 200
- make Fig5b_unary_vs_binary700: to generate the results for the unary vs binary case study with initial state 700
- make models: to compile all models
The following command compiles dot files into pdf files:
- make pdf