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

Fast R implementation of Gillespie's Stochastic Simulation Algorithm

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

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.

Gillespie Codes on Lattices in C++

Implementation of Gillespie Stochastic Simulation Algorithm

Evolutionary models of extrachromosomal DNA (ecDNA).

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

Dynamic Boltzmann Machine for Lattice Chemical Kinetics

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