Stochastic Simulation of SRN models

This is an implementation of stochastic simulation techniques for models of stochastic reaction networks.

Dependencies & Compilation

To compile and run this code one needs to install

• the nightly rust toolchain
• Python 3 and Sympy

With these dependencies in place cargo build --release should suffice to build the code.

Model specification language

Models such as a birth-death process can be modelled as follows.

parameters
  a = 10
  b = 0.1

species X

reactions
  0 -> X @ a;
  X -> 0 @ b * X;

init
  X = 0

More examples can be found in the models directory.

Usage

The tools options are best documented via the --help flag.