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: 13 Apr 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: 29 Nov 2024
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: 10 Jan 2025
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: 19 Nov 2024
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/mmariani123/ctmc_project
My current main work in progress which will probably branch into a second population genetics paper (solely deterministic here). CTMC malaria life-cycle SSA (stochastic) modelling project with potential CLI or Shiny UI. Mostly MALAB and Rust with some Python3 and C. See my main collaborator's faculty page: Potential employers are free to contact.
genetics gillespie-algorithm matlab parasitology rust statistics stochastic
Last synced: 13 Mar 2025
