Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
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Updated
Jul 26, 2024 - Julia
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Finite State Projection algorithms for chemical reaction networks
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
🌲 a flexible gene expression simulator with codon-specific translation rates
DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays
Networkx implementation of the SIS epidemic model for large and heterogeneous networks
Implementation of SIS epidemic model for large and heterogeneous networks
Implementation of TASEP with reinitiation and particles of arbitrary size.
Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.
Simulating and Optimising Dynamical Models in Python 3
A free, open-source tool for modeling chemical reaction networks in Python
A Matlab library of numerical methods for solving differential equations stochastically and continuously .
Final Project for a Mathematical Biology course
Models for Biochemical and Biophysical Research Communications manuscript
Stochastic implementation of a Lotka-Volterra competition model extended to multidimensional niche spaces (published in 10.1103/PhysRevE.91.052107)
Working with Gillespie algorithm in order to exam Double step gene expression model.
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