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

Openfoam library for physiological flow. Solvers and boundary conditions.

BioEn - Bayesian Inference Of ENsembles

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.

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

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

🔮 Predict DNA assembly clone validity rates - powered by Kappa

Biological evolution simulator

A Hodgkin-Huxley model visualization for a neural tree