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SciML / Catalyst.jl

Sponsor

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 dsl systems-biology ode reaction-network differential-equations sde chemical-reactions gillespie-algorithm systems-biology-simulation rate-laws scientific-machine-learning sciml

Updated Mar 19, 2022
Julia

darrenjw / smfsb

Star

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

systems-biology inference mcmc sbml gillespie-algorithm

Updated Oct 31, 2021
AMPL

augustinas1 / MomentClosure.jl

Star

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

systems-biology moments chemical-reaction-networks stochastic-processes gene-network gillespie-algorithm moment-equations moment-closure

Updated Feb 11, 2022
Julia

SciML / ReactionNetworkImporters.jl

Sponsor

Star

Catalyst.jl importers for various reaction network file formats.

biology julia chemical-kinetics differential-equations chemical-reactions gillespie-algorithm

Updated Mar 15, 2022
Julia

kaandocal / FiniteStateProjection.jl

Star

Finite State Projection algorithms for chemical reaction networks

systems-biology julia-package chemical-reaction-networks gene-network gillespie-algorithm stochastic-simulations biological-modeling finite-state-projection

Updated Mar 14, 2022
Julia

SciML / SBMLToolkit.jl

Sponsor

Star

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

systems-biology ode differential-equations chemical-reaction-networks sbml gillespie-algorithm quantitative-systems-pharmacology sciml

Updated Mar 10, 2022
Julia

wcota / dynSIS-networkx

Star

Networkx implementation of the SIS epidemic model for large and heterogeneous networks

networkx computational-physics complex-networks epidemics stochastic-processes stochastic-simulation-algorithm markovian-epidemic-processes gillespie-algorithm markovian-processes

Updated Mar 4, 2022
Python

clauswilke / pinetree

Star

🌲 a flexible gene expression simulator with codon-specific translation rates

translation gene-expression transcription codons gillespie-algorithm stochastic-simulation

Updated Nov 25, 2020
C++

palmtree2013 / DelaySSAToolkit.jl

Star

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

systems-biology stochastic-process chemical-reaction-networks stochastic-simulation-algorithm gene-network gillespie-algorithm delay-systems

Updated Feb 19, 2022
Julia

ADicksonLab / OpenRXN

Star

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

reactions reaction-diffusion pharmacokinetics gillespie gillespie-algorithm compartmental-models

Updated Jan 24, 2020
Python

shehio / Computational-Biology

Star

viterbi-algorithm computational-biology gene-expression smith-waterman alternative-splicing gradient-descent differential-expression gillespie genome-analysis gradient-descent-algorithm bowtie2 differential-analysis single-cell-genomics gillespie-algorithm single-cell-analysis gradient-descent-implementation genome-alignment viterbi-decoder smith-waterman-alignment differential-expression-analysis

Updated Dec 21, 2019
Jupyter Notebook

wcota / dynSIS

Star

Implementation of SIS epidemic model for large and heterogeneous networks.

networkx computational-physics complex-networks epidemics stochastic-processes stochastic-simulation-algorithm markovian-epidemic-processes gillespie-algorithm markovian-processes

Updated Mar 4, 2022
Fortran

lewlin / Stochastic-multidimensional-LV

Star

Stochastic implementation of a Lotka-Volterra competition model extended to multidimensional niche spaces (published in 10.1103/PhysRevE.91.052107)

stochastic-processes lotka-volterra montecarlo-simulation gillespie-algorithm

Updated Apr 13, 2018
C

JacobHilbert / simple-gillespie

Star

Gillespie algorithm implementing the ARN-Protein model for multiple cells.

cpp simulation parallel openmp gillespie-algorithm

Updated Jun 10, 2020
C++

KeepFloyding / numericalMethodsMat

Star

A Matlab library of numerical methods for solving differential equations stochastically and continuously .

matlab stochastic numerical-methods runge-kutta gillespie-algorithm

Updated Nov 12, 2017
MATLAB

Gdemaude / Gillespie

Star

Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes

epidemiology numba stochastic-processes gillespie-algorithm sir-model

Updated Apr 28, 2021
Python

MrsYuuki / Gillespie_stoch_model

Star

Working with Gillespie algorithm in order to exam Double step gene expression model.

python pandas matplotlib gillespie-algorithm

Updated Apr 1, 2021
Python

qvhaelen / typhon

Star

automatized generation of optimized Gillespie algorithm

dependency-graph data-structures binary-search-tree nonlinear-dynamics temporal-data kinetic-modeling reduction-strategies gillespie-algorithm pathway-models

Updated Aug 18, 2018
Fortran

wcota / dynSIS-py

Star

Implementation of SIS epidemic model for large and heterogeneous networks

networkx computational-physics complex-networks epidemics stochastic-processes stochastic-simulation-algorithm markovian-epidemic-processes gillespie-algorithm markovian-processes

Updated Mar 4, 2022
Python

edbonneville / gillespie-shiny

Star

Shiny app simulating stochastic epidemics with Gillespie's direct method.

shiny shinydashboard gillespie-algorithm epidemic-simulations

Updated Jul 30, 2019
R

nsdumont / Spatial-Epidemics-Dynamics-and-Synchronization

Star

Final Project for a Mathematical Biology course

disease-spread mathematical-biology gillespie-algorithm sychrony seasonality sir-model

Updated Aug 4, 2017
TeX

voduchuy / KrylovFspSsa

Star

Fortran implementation of the Krylov-FSP-SSA algorithm for solving the Chemical Master Equation.

numerical-methods stochastic-simulation-algorithm gillespie-algorithm krylov-subspace-approximation chemical-master-equation stochastic-reaction-networks

Updated Jul 29, 2021
Fortran

durs125 / BioResearch

Star

Delay Gillespie Degrade and Fire with variable delay

biology mathematics mathematical-modelling gillespie-algorithm

Updated Feb 11, 2021
Python

snsinfu / cxx-distr

Star

Efficient discrete random distribution for C++. The implementation uses array-based sum tree to allow fast sampling and updates of weighted events.

c-plus-plus distribution random kinetic-monte-carlo header-only gillespie-algorithm sum-tree

Updated Dec 28, 2020
C++

j-lazo / population_models

Star

cellular-automata population-model gillespie-algorithm stochastic-models lotka-volterra-model

Updated Apr 18, 2019
Python

vsukhor / utils

Star

A collection of some handy utilities

library cmake graph-theory configuration-files gillespie-algorithm

Updated Aug 3, 2021
C++

mauricelanghinrichs / memocell

Star

Bayesian inference of stochastic cellular processes with and without memory in Python.

python markov-model statistical-inference model-selection biological-data-analysis dynamical-systems parameter-estimation bayesian-inference nested-sampling stochastic-processes probabilistic-models gillespie-algorithm stochastic-models master-equation biological-modeling

Updated May 25, 2021
Python

physics-based-ml / LatticeGillespieCpp

Star

Gillespie Codes on Lattices in C++

simulations lattice gillespie gillespie-algorithm

Updated Jul 6, 2021
Mathematica

marvinboe / reTASEP

Star

Implementation of TASEP with reinitiation and particles of arbitrary size.

gillespie-algorithm rna-translation tasep

Updated Apr 18, 2016
C++

ctogle / mini_gillespiem

Star

Scalable stochastic simulation of chemical networks

stochastic-simulation-algorithm gillespie-algorithm

Updated Jun 4, 2020
Jupyter Notebook

gillespie-algorithm

Here are 35 public repositories matching this topic...

SciML / Catalyst.jl

darrenjw / smfsb

augustinas1 / MomentClosure.jl

SciML / ReactionNetworkImporters.jl

kaandocal / FiniteStateProjection.jl

SciML / SBMLToolkit.jl

wcota / dynSIS-networkx

clauswilke / pinetree

palmtree2013 / DelaySSAToolkit.jl

ADicksonLab / OpenRXN

shehio / Computational-Biology

wcota / dynSIS

lewlin / Stochastic-multidimensional-LV

JacobHilbert / simple-gillespie

KeepFloyding / numericalMethodsMat

Gdemaude / Gillespie

MrsYuuki / Gillespie_stoch_model

qvhaelen / typhon

wcota / dynSIS-py

edbonneville / gillespie-shiny

nsdumont / Spatial-Epidemics-Dynamics-and-Synchronization

voduchuy / KrylovFspSsa

durs125 / BioResearch

snsinfu / cxx-distr

j-lazo / population_models

vsukhor / utils

mauricelanghinrichs / memocell

physics-based-ml / LatticeGillespieCpp

marvinboe / reTASEP

ctogle / mini_gillespiem

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