The Tau-Splitting algorithm

The Tau-Splitting algorithm is an algorithm for the simulation of chemical reaction networks.

Installation

Executables for Windows and Linux are available in the Releases section of the GitHub repository. Alternatively, to compile the progrm from the source code, first install the Rust programming language, which can be installed from the official website. After Rust is installed, the Tau-Split algorithm can be installed by typing cargo install tausplit in the command line, or by cloning the repository and running cargo install --path . in the repository directory.

Once the executable is downloaded, open the command line in the directory where the executable was downloaded. The basic usage is

tausplit.exe {time} {input_file}

if the Windows executable was downloaded, or

tausplit {time} {input_file}

if the Linux executable was downloaded, or if the program was downloaded using cargo install tausplit. Future examples will use the Linux syntax.

The command simulates the chemical reaction network specified in the input file for the specified time period, and output a TSV containing the initial and final states of the system. The TSV has one column for the sample time and one column for each molecular species, and one row for each sampled time point. Every cell contains the number of molecules from the given molecular species at the sampled time.

Example files

Example files for chemical reaction networks can be found in the data/test_models directory of the GitHub repository. More examples for chemical reaction networks, including the B-cell receptor network and the FceRI network, can be downloaded from https://www.cosbi.eu/prototypes/rssa, under "Collection of models".

If the example file synthesis.txt is placed in the same directory as the tausplit executable, the progress of the network over a period of 5 seconds can be simulated using

tausplit 5 synthesis.txt

Options

-s {count}, --samples {count}

Samples the state of the system count evenly spaced times. If time is 40 and count is 4, the algorithm will sample the system at 10, 20, 30, and 40 and output the states at those times in the TSV.

--algorithm {algorithm}

Uses the given algorithm to simulate the system. The currently supported algorithms are tau-split, tau-split6, and gillespie. The default algorithm is tau-split, which is an optimized version of the algorithm described in the manuscript.

--seed {seed}

Uses the given seed for random number generation during the algorithm's run.

--count-reactions

Adds the total number of reactions to the TSV produced.

--cpu-time

Adds the total runtime of the algorithm to the TSV produced.

--no-print-state

Makes the program not include the state of the system in the TSV produced.

Input format

The chemical reaction networks are specified by files in the following format:

A = 5
B = 3
C = 0
D = 0

A + B -> C + 3D, 3.5

Rows of the format A = 5 define that a chemical species A exists, and that its amount at the beginning of the simulation is 5. Rows of the format A + B -> C + 3D, 3.5 define the chemical reaction in which A and B react to form one C and three Ds, with a rate constant of 3.5. The reaction network can be split across any number of files, allowing using the same chemical reaction network with different initial states.

Lines starting with # are treated as comments, and are not parsed.