# 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.

## Install

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

- Launch Julia's REPL (for example by entering
`julia`

in the shell) - Enter Pkg's REPL by typing
`]`

- 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.