BiochemNetABC.jl

Documentation

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.

Install

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

Getting started

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

Tests

Execution and statistical tests can be run through:

julia test/runtests.jl

or in Pkg's REPL:

pkg> test BiochemNetABC

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

Benchmarks

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

Info

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