Projects in Awesome Lists tagged with gillespie-algorithm
A curated list of projects in awesome lists tagged with gillespie-algorithm .
https://github.com/sciml/catalyst.jl
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
biology chemical-reactions differential-equations dsl gillespie-algorithm julia ode rate-laws reaction-network scientific-machine-learning sciml sde simulation systems-biology systems-biology-simulation
Last synced: 14 May 2025
https://github.com/SciML/Catalyst.jl
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
biology chemical-reactions differential-equations dsl gillespie-algorithm julia ode rate-laws reaction-network scientific-machine-learning sciml sde simulation systems-biology systems-biology-simulation
Last synced: 30 Mar 2025
https://github.com/augustinas1/MomentClosure.jl
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
chemical-reaction-networks gene-network gillespie-algorithm moment-closure moment-equations moments stochastic-processes systems-biology
Last synced: 22 Jul 2025
https://github.com/sciml/sbmltoolkit.jl
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
chemical-reaction-networks differential-equations gillespie-algorithm julia ode quantitative-systems-pharmacology sbml sciml systems-biology
Last synced: 06 May 2025
https://github.com/darrenjw/smfsb
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
gillespie-algorithm inference mcmc sbml systems-biology
Last synced: 21 Jun 2025
https://github.com/sciml/finitestateprojection.jl
Finite State Projection algorithms for chemical reaction networks
biological-modeling chemical-reaction-networks finite-state-projection gene-network gillespie-algorithm julia-package stochastic-simulations systems-biology
Last synced: 21 Oct 2025
https://github.com/adicksonlab/openrxn
A free, open-source tool for modeling chemical reaction networks in Python
compartmental-models gillespie gillespie-algorithm pharmacokinetics reaction-diffusion reactions
Last synced: 16 Jan 2026
https://github.com/clauswilke/pinetree
🌲 a flexible gene expression simulator with codon-specific translation rates
codons gene-expression gillespie-algorithm stochastic-simulation transcription translation
Last synced: 22 Mar 2025
https://github.com/twallema/pysodm
Simulating and Optimising Dynamical Models in Python 3
emcee gillespie-algorithm integration-flow model-calibration modelling-framework ordinary-differential-equations simulation xarray
Last synced: 20 Mar 2025
https://github.com/wangl-cc/evolutionarymodelingtools.jl
Simulate evolutionary biology models with Gillespie algorithm.
ecology evolution evolutionary-dynamics gillespie-algorithm julia simulation
Last synced: 15 May 2025
https://github.com/edbonneville/gillespie-shiny
Shiny app simulating stochastic epidemics with Gillespie's direct method.
epidemic-simulations gillespie-algorithm shiny shinydashboard
Last synced: 25 Oct 2025
https://github.com/mauricelanghinrichs/memocell
Bayesian inference of stochastic cellular processes with and without memory in Python.
bayesian-inference biological-data-analysis biological-modeling dynamical-systems gillespie-algorithm markov-model master-equation model-selection nested-sampling parameter-estimation probabilistic-models python statistical-inference stochastic-models stochastic-processes
Last synced: 13 Apr 2025
https://github.com/voduchuy/krylovfspssa
Fortran implementation of the Krylov-FSP-SSA algorithm for solving the Chemical Master Equation.
chemical-master-equation gillespie-algorithm krylov-subspace-approximation numerical-methods stochastic-reaction-networks stochastic-simulation-algorithm
Last synced: 20 Jan 2026
