Build and simulate jump equations like Gillespie simulations and jump diffusions with constant and state-dependent rates and mix with differential equations and scientific machine learning (SciML)

Fast stochastic simulator for chemical reaction networks

Python package for stochastic simulations

A free, open-source tool for modeling chemical reaction networks in Python

Stochastic simulator of mitochondria represented as a dynamic spaceless graph

Gillespie simulations on a 2D lattice, featuring spatial oscillations

Fast R implementation of Gillespie's Stochastic Simulation Algorithm

Project for Physical Methods of Biology based on Kim JK, Tyson JJ (2020) Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy. PLoS Comput Biol 16(10): e1008258. https://doi.org/10.1371/journal. pcbi.1008258.

This repository contains codes developed in 2022 to simulate the biofilm formation with the proposed stochastic model based on quorum sensing and chemical reactions.

Simple as it gets Gillespie library in C++, as a stepping stone for your own Gillespie codes

A brief presentation done by me on Gillespie's paper and algorithm about biochemical stochastic simulations

Evolutionary models of extrachromosomal DNA (ecDNA).

Dynamic Boltzmann Machine for Lattice Chemical Kinetics

Library of different simulation methods

Gillespie Codes on Lattices in C++

Implementation of Gillespie Stochastic Simulation Algorithm

Some tools for performing Monte Carlo simulations of chemical reaction networks in my research

Stochastic simulation of Enzyme kinetics at work