biological-simulations
There are 88 repositories under biological-simulations topic.
brian-team/brian2
Brian is a free, open source simulator for spiking neural networks.
opensim-org/opensim-core
SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.
rileyjshaw/terra
:space_invader: JS library for simple biological simulations and cellular automata
BlueBrain/BluePyOpt
Blue Brain Python Optimisation Library
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.
brian-team/brian2cuda
A brian2 extension to simulate spiking neural networks on GPUs
DamCB/tyssue
An epithelium simulation library
biosimulations/biosimulations
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
PMEAL/pytrax
Random walk to calculate the tortuosity tensor of images
brainpy/examples
Examples of BrainPy
KeepFloyding/OpenFOAM-phys-flow
Openfoam library for physiological flow. Solvers and boundary conditions.
bio-phys/BioEn
BioEn - Bayesian Inference Of ENsembles
souvik1982/Brain
Simulating a primordial brain. A biological (spiking) neural network structuring itself through natural selection.
tzeitim/genome-blender
Scripts to create cartoons of 3D genomes
ali-ramadhan/lagrangian-microbes
🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.
hammouc/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
LS-2ednar/OpenFOAM_Programming
Programming with OpenFOAM is explained with a follow-along approach.
Edinburgh-Genome-Foundry/kappagate
:crystal_ball: Predict DNA assembly clone validity rates - powered by Kappa
Axelwickm/NeuroCorrelation
3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)
PascalCorpsman/biosim4_FPC_translation
Biological evolution simulator
pchlenski/misdeed
Microbiome data simulator for power analysis
v--/neuronsim
A Hodgkin-Huxley model visualization for a neural tree
programandoconro/Simulaciones-de-epidemias
Simulaciones de epidemias 👾 en poblaciones con mezclas homogéneas 👪 utilizando modelos basados en agentes autónomos 🤖
Bluejee/MNEST
MNEST (Multi-agent Neuro Evolution Simulation Toolkit) is a software framework designed to model and study emergent behavior in complex systems.
Edinburgh-Genome-Foundry/topkappy
:waxing_gibbous_moon: Pythonic bindings for the Kappa model simulation language
kiwijuice56/evolution-simulation
Interactive game to simulate emergence and natural selection in biological systems
Empoliam/Pottchi
Cellular Potts Model implemented in C++
rwill128/evo-sim-cuda-python
An evolution simulation inspired by Biogenesis on Sourceforge.
BjornFJohansson/ypkpathway
Automatic pathway assembly with the YeastPathwayKit
gildiamant31/Computational_Biology-
Computational Biology Course
jsutlive/Cell-Mechanics-Simulator
A simple mechanics-based approach to simulating cells. Uses a component-based GUI approach
kernelshreyak/livmach
An organism simulation framework based on cell growth and resultant emergent phenomena.
melnyashka/horizontal_gene_transfer
Cemracs 2018 project (CIRM, July-August 2018)
BrosnanYuen/RayBNN_Cell
Cell Position Generator for RayBNN
Thokas99/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.