Finite State Projection algorithms for chemical reaction networks

Python package for stochastic simulations

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

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

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

Implementation of Gillespie Stochastic Simulation Algorithm

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.

Tutorial for Statistical Inference with Julia.

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.

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.