BioSimulator.jl
A stochastic simulation framework for Julia.
Introduction
Many complex systems in biology are analytically intractable, and dynamical predictions based on deterministic models can be grossly misleading. Stochastic simulation algorithms based on continuous-time Markov chains allow researchers to generate accurate time-evolution trajectories, test the sensitivity of models to key parameters, and quantify frequencies of rare events.
Situations where stochastic simulation is especially helpful involve:
- rare events such as extinction and mutation,
- key molecules present in small numbers,
- rare reactions with dramatic influence on the dynamics of the system
- population cycles arising from demographic stochasticity.
Examples of such systems include gene expression networks, tumor suppressor pathways, and demographic and ecological systems.
BioSimulator.jl aims to provide researchers interested in such phenomena with a fast, reliable, user-friendly, and open-source modeling tool in Julia.
Installation
BioSimulator.jl can be installed with Julia's package manager at the REPL (note the capitalization in URLs):
Option 1: Directly with Pkg
using Pkg
Pkg.add("https://github.com/alanderos91/BioSimulator.jl.git")Option 2: Press ] to enter pkg mode and enter the following:
pkg> add https://github.com/alanderos91/BioSimulator.jl.gitYou can start using BioSimulator.jl in scripts or the REPL with the command:
using BioSimulator