SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
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Updated
May 28, 2024 - C++
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.
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
Brian is a free, open source simulator for spiking neural networks.
Blue Brain Python Optimisation Library
👾 JS library for simple biological simulations and cellular automata
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.
An epithelium simulation library
Random walk to calculate the tortuosity tensor of images
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
A brian2 extension to simulate spiking neural networks on GPUs
Openfoam library for physiological flow. Solvers and boundary conditions.
Examples of BrainPy
MNEST (Multi-agent Neuro Evolution Simulation Toolkit) is a software framework designed to model and study emergent behavior in complex systems.
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
Simulaciones de epidemias 👾 en poblaciones con mezclas homogéneas 👪 utilizando modelos basados en agentes autónomos 🤖
Model, Data, and Analysis Scripts for "The Evolution of Cooperation by the Hankshaw Effect"
HOME OF THE 2-SPEED GENOME MODEL
Project for the course of Laboratory Mathematical Modelling held by Professor Marchetti (A.Y. 2023-2024) for the master curse Quantitative and Computational Biology (QCB) at university of Trento, italy.
A Hodgkin-Huxley model visualization for a neural tree