Biological Simulation is the use of computational and mathematical models to simulate biological systems. The underlying complexity of biology necessitates the development of efficient algorithms, knowledge representation methods, visualization techniques, data formats, and computational tools to observe the emergent behaviors of biological systems. The broad scope and variety of time-scales and space-scales requires development of community-driven standards and common formats to enable interoperability and reproducibility of models.
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.
🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.
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
🔮 Predict DNA assembly clone validity rates - powered by Kappa
Biological evolution simulator
A Hodgkin-Huxley model visualization for a neural tree