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

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

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

Simplest simulation to use non-Exponential transitions

Simulating and Optimising Dynamical Models in Python 3

Simulate evolutionary biology models with Gillespie algorithm.

No description provided.

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

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

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

No description provided.

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).

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

An mRNA reaction scheme simulator using the Doob-Gillespie algorithm in R

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

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

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

This project provides rigorous Python codes for simulating the stochastic movement of kinesin protein on a microtubule.

automatized generation of optimized Gillespie algorithm

Stochastic Simulator of Chemical Reactions

Implementation of Gillespie Stochastic Simulation Algorithm