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 500augustinas1 / MomentClosure.jl
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Language:Julia 46SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Language:Julia 44darrenjw / smfsb
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
Language:AMPL 32Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices
Language:Julia 27Finite State Projection algorithms for chemical reaction networks
Language:Julia 20wcota / dynSIS-networkx
Networkx implementation of the SIS epidemic model for large and heterogeneous networks
Language:Python 18xiaomingfu2013 / DelaySSAToolkit.jl
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Language:Julia 17ADicksonLab / OpenRXN
A free, open-source tool for modeling chemical reaction networks in Python
Language:Python 13clauswilke / pinetree
🌲 a flexible gene expression simulator with codon-specific translation rates
Language:C++ 12- Language:Python 10
Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.
Language:Fortran 10wangl-cc / EvolutionaryModelingTools.jl
Simulate evolutionary biology models with Gillespie algorithm.
Language:Julia 8adolgert / CompetingClocks.jl
Simplest simulation to use non-Exponential transitions
Language:Julia 6shehio / 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 4- Language:Python 3
edbonneville / 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 2KeepFloyding / numericalMethodsMat
A Matlab library of numerical methods for solving differential equations stochastically and continuously .
Language:Matlab 2- Language:Python 2
TomMakesThings / Gillespie-mRNA-Simulator
An mRNA reaction scheme simulator using the Doob-Gillespie algorithm in R
Language:HTML 2fatihguelec / Stochastic-Biofilm-Disruption-Model-Based-on-Quorum-Sensing-Mimickers
This repository contains codes developed in 2022 to simulate the bacterial biofilm formation with the proposed stochastic biofilm disruption model based on quorum sensing mimickers and chemical reactions.
Language:MATLAB 1jacons / Chemical-Reactions-Simulator
Stochastic Simulator of Chemical Reactions
Language:Python 1locuoco / stochastic-chemical-kinetics
Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics
Language:C++ 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++ 1Theophilus-Dwamena / Continuous-time-Markov-model-for-kinesin-stepping
This project provides rigorous Python codes for simulating the stochastic movement of kinesin protein on a microtubule.
Language:Jupyter Notebook 1VishvasRanjan / Learning-Chemical-Reaction-Networks-CRNs
This repository contains the work that was conducted under the joint supervision of Dr. Behera and Prof. Sbalzarini at the Sbalzarini Lab, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD).
Language:Jupyter Notebook 1adityak714 / scientific-computations
A collection of projects done individually, and with a peer, in Stochastic and Deterministic Simulations, Least Squares Analysis, and the usage of Singular Value Decomposition for Low-Rank Image Compression, as well as in Pattern Recognition, as part of a master's level course in Scientific Computing at Uppsala University.
Language:Jupyter Notebook 0louisreese / CrisprCutSim
Stochastic simulation of CRISPR nucleases cleaving a pool of DNA or RNA
Language:C++ 0- Language:Mathematica 0
Stochastic simulation of Enzyme kinetics at work
Language:Jupyter Notebook 0karthik-d / dynamical-modeling-of-biological-systems
Bottom-up dynamical modeling of biological systems using ordinary, partial, and stochastic differential equations.
Language:MATLAB
