BiochemNetABC.jl

A Julia package for efficient simulation, statistical inference and verification of Markov Processes/Continuous Time Markov Chains (CTMC) modeled by Biochemical networks/Chemical Reaction Networks (CRN) with Approximate Bayesian Computation methods (ABC).

It implements:

• A core for simulation of Markov Processes/CTMC,
• A simple interface for Biochemical Networks/Stochastic Petri Nets,
• Synchronized simulation with Linear Hybrid Automata.
• Approximate Bayesian Computation (a likelihood-free inference method),
• Automaton-ABC: a statistical method for verification of parametric CTMC.

This package is not yet registered in the Julia's General registry. For the install of the package:

1. Launch Julia's REPL (for example by entering julia in the shell)
2. Enter Pkg's REPL by typing ]
3. Enter

   pkg> add https://github.com/bentriom/BiochemNetABC.jl

A few notebooks are available in examples/notebooks for a quick presentation of the packages' features.

Execution and statistical tests can be run through:

julia test/runtests.jl

or in Pkg's REPL:

pkg> test BiochemNetABC

⚠️ The statistical tests run by test/run_cosmos.jl needs Cosmos in your PATH environment variable.

Benchmarks have been made to test the package performance compared to well-known efficient other packages such as DifferentialEquations.jl.

The mathematical fundations and the package architecture are presented in my PhD thesis.