Brian is a free, open source simulator for spiking neural networks.

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

👾 JS library for simple biological simulations and cellular automata

Blue Brain Python Optimisation Library

Evoplex is a fast, robust and extensible platform for developing agent-based models and multi-agent systems on networks. It's available for Windows, Linux and macOS.

A brian2 extension to simulate spiking neural networks on GPUs

An epithelium simulation library

A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

Random walk to calculate the tortuosity tensor of images

Examples of BrainPy

BioEn - Bayesian Inference Of ENsembles

Openfoam library for physiological flow. Solvers and boundary conditions.

Simulating a primordial brain. A biological (spiking) neural network structuring itself through natural selection.

Scripts to create cartoons of 3D genomes

Programming with OpenFOAM is explained with a follow-along approach.

🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.

🔮 Predict DNA assembly clone validity rates - powered by Kappa

This repository includes Matlab codes/routines that were used in our manuscript entitled "Importance sampling for a robust and efficient multilevel Monte Carlo estimator for stochastic reaction networks" that can be found in this preprint: https://arxiv.org/abs/1911.06286

Biological evolution simulator

A Hodgkin-Huxley model visualization for a neural tree