A Mathematica package for working with networks of coupled chemical reactions. It forms a foundation for syntactic manipulation of chemical reaction networks as Mathematica expressions. It allows mixing and matching mass-action kinetics with other kinds of dynamics, and provides a simple way to simulate experiments in which a sequence of chemical additions is performed. It is particularly well-suited for engineered chemical systems, in which chemical reaction networks can be used as a kind of "programming language".
See Examples.nb for the kind of things it can do.
- Package: CRNSimulator.m
- Extensions: CRNSimulatorExtensions.m (needed for some more advanced features)
- Examples: Examples.nb
Extends CRNSimulator to perform Gillespie SSA simulation. The main simulation loop is compiled to C code for speed. Input reactions and initial counts using the same syntax as CRNSimulator.
See ExamplesSSA.nb for simple examples.
- Package: CRNSimulatorSSA.m (requires CRNSimulator package)
- Examples: ExamplesSSA.nb