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
Examples of BrainPy
Random walk to calculate the tortuosity tensor of images
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
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
Programming with OpenFOAM is explained with a follow-along approach.
🔮 Predict DNA assembly clone validity rates - powered by Kappa
🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.
A Hodgkin-Huxley model visualization for a neural tree
Biological evolution simulator