Finite State Projection algorithms for chemical reaction networks

Python package for stochastic simulations

A Julia implementation of Gillespie's algorithm(s).

Tools for data generation and data analysis for the eLife research article - "The solubility product extends the buffering concept to heterotypic biomolecular condensates"

Software supporting M. Cavallaro, et al., 3′-5′ crosstalk contributes to transcriptional bursting. Genome Biol 22, 56 (2021). https://doi.org/10.1186/s13059-020-02227-5

A glimpse of some stochastic simulation methods. I don't claim originality for the results posted here: these are mostly some quick experiments I did while doing research.

Implementation of Gillespie Stochastic Simulation Algorithm

Modigliani is a stochastic simulation framework for neuroscientists

An implementation of a pratical guide to stochastic simulations of reaction-diffusion processes

Code for the paper "Bistability in Type I Toxin-Antitoxin Systems May Lead to Stress-Induced Persister Formation" by Sofija Markovic, Magdalena Djordjevic, Hong-Yu OU, and Marko Djordjevic.

Tutorial for Statistical Inference with Julia.

Numba accelerated and multiprocess simulation of propagation of the African Swine Fever Virus

Simulation and kernel density estimation of linear and non-linear stochastic systems. Some codes include the computation of the information rate, KL-divergence and information length.