biological-simulations
There are 10 repositories under biological-simulations topic.
- brian2
brian-team / brian2
Brian is a free, open source simulator for spiking neural networks.
Language:Python 921 opensim-org / opensim-core
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
Language:C++ 778rileyjshaw / terra
:space_invader: JS library for simple biological simulations and cellular automata
Language:JavaScript 610- BluePyOptLanguage:Python 198
evoplex / evoplex
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.
Language:C++ 133A brian2 extension to simulate spiking neural networks on GPUs
Language:Python 60- Language:Python 58
- biosimulations
biosimulations / biosimulations
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
Language:TypeScript 38 - Language:Python 28
- Language:Jupyter Notebook 21
- Language:Python 16
KeepFloyding / OpenFOAM-phys-flow
Openfoam library for physiological flow. Solvers and boundary conditions.
Language:C++ 16souvik1982 / Brain
Simulating a primordial brain. A biological (spiking) neural network structuring itself through natural selection.
Language:C++ 13tzeitim / genome-blender
Scripts to create cartoons of 3D genomes
Language:Python 13ali-ramadhan / lagrangian-microbes
🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.
Language:Python 10hammouc / Multilevel-Monte-Carlo-with-Importance-Sampling-for-SRNs
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
Language:MATLAB 10Edinburgh-Genome-Foundry / kappagate
:crystal_ball: Predict DNA assembly clone validity rates - powered by Kappa
Language:Python 9LS-2ednar / OpenFOAM_Programming
Programming with OpenFOAM is explained with a follow-along approach.
Language:C++ 9Axelwickm / NeuroCorrelation
3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)
Language:C++ 7PascalCorpsman / biosim4_FPC_translation
Biological evolution simulator
Language:Pascal 7- Language:Jupyter Notebook 7
- Language:D 7
Bluejee / MNEST
MNEST (Multi-agent Neuro Evolution Simulation Toolkit) is a software framework designed to model and study emergent behavior in complex systems.
Language:Python 6- Simulaciones-de-epidemias
programandoconro / Simulaciones-de-epidemias
Simulaciones de epidemias 👾 en poblaciones con mezclas homogéneas 👪 utilizando modelos basados en agentes autónomos 🤖
Language:R 6 :waxing_gibbous_moon: Pythonic bindings for the Kappa model simulation language
Language:Python 5kiwijuice56 / evolution-simulation
Interactive game to simulate emergence and natural selection in biological systems
Language:Java 5- Language:C++ 3
rwill128 / evo-sim-cuda-python
An evolution simulation inspired by Biogenesis on Sourceforge.
Language:Jupyter Notebook 3BjornFJohansson / ypkpathway
Automatic pathway assembly with the YeastPathwayKit
Language:Python 2gildiamant31 / Computational_Biology-
Computational Biology Course
Language:Python 2jsutlive / Cell-Mechanics-Simulator
A simple mechanics-based approach to simulating cells. Uses a component-based GUI approach
Language:Java 2kernelshreyak / livmach
An organism simulation framework based on cell growth and resultant emergent phenomena.
Language:C++ 2- Language:HTML 2
melnyashka / horizontal_gene_transfer
Cemracs 2018 project (CIRM, July-August 2018)
Language:Python 2punamrattu / computational_biophysics
Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).
Language:Shell 2Thokas99 / Laboratory_of_Mathematical_Modelling
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.
Language:Python 1
