BioSimulator.jl

BioSimulator.jl is a software package designed for stochastic simulation of biological systems, including those with complex feedback loops and rare events like mutations and extinctions. Developed in the Julia programming language, known for its high performance in scientific computing, this package supports the Gillespie algorithm, tau-leaping, and other related stochastic simulation methods based on Markov chain theory. Features include the ability to diagram Petri Nets for interaction representation, plot average trajectories with standard deviations, and generate frequency distributions for species at specified times. BioSimulator.jl allows users to build models within Julia programmatically and then simulate and analyze outcomes with built-in visualization and statistical tools. Its user-friendly approach aims to facilitate stochastic simulation use, streamline model development, and minimize errors in model specification, catering to a wide range of complexities from various fields like ecology, systems biology, chemistry, and genetics.