A stochastic simulation framework for Julia.
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.
BioSimulator.jl can be installed with Julia's package manager at the REPL (note the capitalization in URLs):
Option 1: Directly with
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.git
You can start using BioSimulator.jl in scripts or the REPL with the command: