gillespie-algorithm

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

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

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

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

Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices

Finite State Projection algorithms for chemical reaction networks

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

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

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

Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.

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

Simplest simulation to use non-Exponential transitions

Simulate evolutionary biology models with Gillespie algorithm.

Simulating and Optimising Dynamical Models in Python 3

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

Implementation of SIS epidemic model for large and heterogeneous networks

Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics

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

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).