gillespie-algorithm
There are 0 repository under gillespie-algorithm topic.
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.
Language:Julia 426augustinas1 / MomentClosure.jl
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Language:Julia 43SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Language:Julia 35darrenjw / smfsb
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
Language:AMPL 31Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices
Language:Julia 26Finite State Projection algorithms for chemical reaction networks
Language:Julia 18wcota / dynSIS-networkx
Networkx implementation of the SIS epidemic model for large and heterogeneous networks
Language:Python 16xiaomingfu2013 / DelaySSAToolkit.jl
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Language:Julia 15ADicksonLab / OpenRXN
A free, open-source tool for modeling chemical reaction networks in Python
Language:Python 12clauswilke / pinetree
🌲 a flexible gene expression simulator with codon-specific translation rates
Language:C++ 9- Language:Python 9
Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.
Language:Fortran 9wangl-cc / EvolutionaryModelingTools.jl
Simulate evolutionary biology models with Gillespie algorithm.
Language:Julia 7shehio / Computational-Biology
computational-biologysmith-watermansmith-waterman-alignmentgillespie-algorithmgillespiegradient-descentgradient-descent-algorithmgradient-descent-implementationgenome-analysisgenome-alignmentdifferential-analysisgene-expressionalternative-splicingdifferential-expressiondifferential-expression-analysissingle-cell-analysissingle-cell-genomicsviterbi-algorithmviterbi-decoderbowtie2Language:Jupyter Notebook 6lewlin / Stochastic-multidimensional-LV
Stochastic implementation of a Lotka-Volterra competition model extended to multidimensional niche spaces (published in 10.1103/PhysRevE.91.052107)
Language:C 4edbonneville / gillespie-shiny
Shiny app simulating stochastic epidemics with Gillespie's direct method.
Language:R 2Gdemaude / Gillespie
Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes
Language:Python 2- Language:Python 2
- Language:Python 2
jacons / Chemical-Reactions-Simulator
Stochastic Simulator of Chemical Reactions
Language:Python 1KeepFloyding / numericalMethodsMat
A Matlab library of numerical methods for solving differential equations stochastically and continuously .
Language:Matlab 1mauricelanghinrichs / memocell
Bayesian inference of stochastic cellular processes with and without memory in Python.
Language:Python 1MrsYuuki / Gillespie_stoch_model
Working with Gillespie algorithm in order to exam Double step gene expression model.
Language:Python 1- Language:Fortran 1
snsinfu / cxx-distr
Efficient discrete random distribution for C++. The implementation uses array-based sum tree to allow fast sampling and updates of weighted events.
Language:C++ 1TomMakesThings / Gillespie-mRNA-Simulator
An mRNA reaction scheme simulator using the Doob-Gillespie algorithm in R
Language:HTML 1juliorodrigues07 / computational_modeling
Computational modeling practical exercises.
Language:Cython 0lillux / gillespie_ssa
Implementation of Gillespie Stochastic Simulation Algorithm
Language:Jupyter Notebook 0locuoco / stochastic-chemical-kinetics
Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics
Language:C++ 0PhyBi / miRNA-negative-feedback
This repository contains code for simulatuing 'miRNA-mediated negative feedback loop' model, given in the manuscript 'Effects of miRNA-mediated negative feedback on gene expression', using Gillespie algorithm
Language:Fortran 0sedaradoykova / BIOL0044_protometabolism_modelling
Code and reading materials related to my BIOL0044 MSci Investigative Project at the Lane Origins lab.
Language:HTML 0syedtaz / vermillion
Fastest stochastic simulator in the West.
Language:Rust 0- Language:Mathematica 0
wh607 / Gillespie-Stochastic-System-Simulation
Code to simulate a stochastic system using the Gillespie algorithm with comparisons to the mean field model and steady state analysis.
Language:MATLAB 0louisreese / CrisprCutSim
Stochastic simulation of CRISPR nucleases cleaving a pool of DNA or RNA
Language:C++TommasoTarchi / stocco
A new implementation of a well-known stochastic model for carcinogenesis, augmented with competition dynamics and spatial structuring.
Language:Python
