gillespie

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

Jump Processes in JAX

A blazing-fast parallel Python engine to simulate stochastic reaction networks, written in Rust

Stochastic simulator of mitochondria represented as a dynamic spaceless graph

Chemical reaction networks in JAX: a lightweight, GPU-optimized Gillespie/SSA simulation library.

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.

Gillespie simulations on a 2D lattice, featuring spatial oscillations

Implementation of Gillespie 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.

Evolutionary models of extrachromosomal DNA (ecDNA).

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

Gillespie Codes on Lattices in C++

One network. Two engines. The same stochastic history. Reproducible Gillespie SIR simulation in Python and C, verified event by event, with measured experiments and sanitizer CI.

Dynamic Boltzmann Machine for Lattice Chemical Kinetics

Library of different simulation methods