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

Human brain cells play Doom (CL1)

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

Examples of BrainPy

Random walk to calculate the tortuosity tensor of images

A LLM-friendly framework for translating dynamical equations to gymnasium-compatible RL environments.

BioEn - Bayesian Inference Of ENsembles

Openfoam library for physiological flow. Solvers and boundary conditions.

Code for Entangled Schrödinger Bridge Matching

Code for Branched Schrödinger Bridge Matching (ICLR 2026)

PeerTree.js An Organic Inspired Network Architecture. Build Apps that scale just by cloning existing nodes for more power..

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

Scripts to create cartoons of 3D genomes

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