biological-simulations

There are 11 repositories under biological-simulations topic.

• brian2

  brian-team / brian2

  Brian is a free, open source simulator for spiking neural networks.

  pythonneurosciencesciencedifferential-equationsspiking-neural-networksbiological-simulationscode-generationsimulation-frameworkbriancomputational-neurosciencebrian2
  Language:Python 994

• opensim-org / opensim-core

  SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

  biological-simulationsbiomechanicscomputational-biologycomputational-scienceengineeringmusculoskeletal-modelssciencesimulation
  Language:C++ 933

• rileyjshaw / terra

  :space_invader: JS library for simple biological simulations and cellular automata

  javascriptcellular-automatabiological-simulationsjs-library
  Language:JavaScript 609
• BluePyOpt

  BlueBrain / BluePyOpt

  Blue Brain Python Optimisation Library

  pythonoptimisationsneuroscienceparametermodellingelectrophysiologyneuronscomputational-neurosciencecross-platformbiological-simulationsevolutionary-algorithmsgenetic-algorithm
  Language:Python 215

• 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.

  multi-agentagentgraphcross-platformevolutionary-game-theoryevolutionary-computationevolutionary-algorithmsevolution-simulatormonte-carlo-simulationagent-based-simulationagent-based-modelingagent-based-modelagent-basedcppbiological-simulationsevoplexsimulationmasabmcellular-automata
  Language:C++ 143

• brian-team / brian2cuda

  A brian2 extension to simulate spiking neural networks on GPUs

  pythonbiological-simulationsbrianbrian2code-generationcomputational-neurosciencedifferential-equationsgpugpu-accelerationneurosciencesciencesimulationsimulation-frameworkspiking-neural-networks
  Language:Python 63

• DamCB / tyssue

  An epithelium simulation library

  biological-simulationsgeometrynotebookpandasvertex
  Language:Python 61
• biosimulations

  biosimulations / biosimulations

  A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

  biologymodelingsimulationstandardssbmlsed-mlvegareproducibilitybiochemical-networksbiosimulationsbiological-simulationsbiosimulation
  Language:TypeScript 42

• PMEAL / pytrax

  Random walk to calculate the tortuosity tensor of images

  random-walkporous-mediaphysics-simulationbiological-simulations
  Language:Python 28

• brainpy / examples

  Examples of BrainPy

  brainpybiological-simulationsbrain-simulationsneural-modeling
  Language:Jupyter Notebook 27

• KeepFloyding / OpenFOAM-phys-flow

  Openfoam library for physiological flow. Solvers and boundary conditions.

  cfdbiological-simulationsfluid-dynamicsboundary-conditionsopenfoam-librarysolveropenfoam
  Language:C++ 19

• bio-phys / BioEn

  BioEn - Bayesian Inference Of ENsembles

  biological-simulationsmolecular-dynamicselectron-paramagnetic-resonancestructural-biologynmrxray-scattering-experimentsbayesian-inferencedeerpeldordata-integrationsaxs
  Language:Python 18

• souvik1982 / Brain

  Simulating a primordial brain. A biological (spiking) neural network structuring itself through natural selection.

  neural-networkgenetic-algorithmartificial-intelligencebiological-simulationsreinforcement-learningevolutionary-algorithmscomputational-neuroscience
  Language:C++ 13

• tzeitim / genome-blender

  Scripts to create cartoons of 3D genomes

  3dmodelsbiologybiological-simulationsgenomeblender3dchromatin-interactionchromatin3dgenometads
  Language:Python 13

• 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

  biological-networksbiological-simulationsimportance-samplingmatlabmonte-carlo-methodsmultilevelmultilevel-modelsmultilevel-monte-carlonumerical-analysisnumerical-simulationsstochastic-biological-systemsstochastic-processstochastic-reaction-networksstochastic-simulation-algorithm
  Language:MATLAB 11

• ali-ramadhan / lagrangian-microbes

  🦐🐟🦈 A framework for simulating millions of interacting Lagrangian particles (or microbes!) in a turbulent ocean.

  ecologybiological-simulationsoceanparticle-simulation
  Language:Python 10

• Edinburgh-Genome-Foundry / kappagate

  :crystal_ball: Predict DNA assembly clone validity rates - powered by Kappa

  synthetic-biologydna-assemblylab-automationsequence-designkappa-languagebiological-simulations
  Language:Python 10

• LS-2ednar / OpenFOAM_Programming

  Programming with OpenFOAM is explained with a follow-along approach.

  cfdbiological-simulations
  Language:C++ 10

• Axelwickm / NeuroCorrelation

  3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)

  simulationneural-networkopenglbiologybiological-simulationsbiological-simulationbiological-networksneuron-simulatorspiking-neural-network
  Language:C++ 7

• Bluejee / MNEST

  MNEST (Multi-agent Neuro Evolution Simulation Toolkit) is a software framework designed to model and study emergent behavior in complex systems.

  biological-simulationscomplex-systemsemergent-behaviorphysics-simulationq-learningreinforcement-learningsimulation
  Language:Python 7

• kiwijuice56 / evolution-simulation

  Interactive game to simulate emergence and natural selection in biological systems

  biologyevolution-simulationsimulationnatural-selectionevolutionbiological-simulationsphysics-simulationphysics-2dcollision-detectioneducationaljava
  Language:Java 7

• PascalCorpsman / biosim4_FPC_translation

  Biological evolution simulator

  freepascallazarus-idebiological-simulationssimulation
  Language:Pascal 7

• pchlenski / misdeed

  Microbiome data simulator for power analysis

  biological-simulationsmicrobial-ecologymicrobiomesimulation-framework
  Language:Jupyter Notebook 7

• v-- / neuronsim

  A Hodgkin-Huxley model visualization for a neural tree

  hodgkin-huxley-modelimpulseneuronsbiological-simulations
  Language:D 7

• openbraininstitute / BluePyOpt

  Blue Brain Python Optimisation Library

  biological-simulationscomputational-neurosciencecross-platformelectrophysiologyevolutionary-algorithmsgenetic-algorithmmodellingneuronsneuroscienceoptimisationparameterpython
  Language:Python 6
• Simulaciones-de-epidemias

  programandoconro / Simulaciones-de-epidemias

  Simulaciones de epidemias 👾 en poblaciones con mezclas homogéneas 👪 utilizando modelos basados en agentes autónomos 🤖

  shiny-rapprsimulationsepidemiaepidemicsagent-based-simulationpopulation-dynamicspopulation-epidemicsbiological-simulationsrandomnesssimulaciones-de-epidemiaspandemichomogenous-mixmachine-learningbiological-simulationpopulationcovidpopulation-modelagentes
  Language:R 6

• Edinburgh-Genome-Foundry / topkappy

  :waxing_gibbous_moon: Pythonic bindings for the Kappa model simulation language

  pythonkappa-languagebiological-simulations
  Language:Python 5

• dxns-hub / harmonic-balancer-project

  A mathematical tuning fork designed to help individuals find balance in various aspects of life. Our tool leverages key principles to optimize performance and efficiency. We also incorporate fundamental mathematical constants like Pi (π), Euler’s number €, Phi (φ), and Psi (ψ) to explore their potential in achieving optimal balance and efficiency.

  aibalancebiological-simulationsbiologyenviornmental-analysisfusionharmonyquantum-algorithmsquantum-computingquantum-mechanicsresonancestructural-engineering
  Language:Python 4

• jsutlive / Cell-Mechanics-Simulator

  A simple mechanics-based approach to simulating cells. Uses a component-based GUI approach

  biological-simulationsphysicsphysics-simulationmorphogenesis
  Language:Java 4

• kirkegaardlab / gradnodes

  Official code implementation of the paper on adaptive node position in biological transport networks

  biological-simulationsdifferentiable-physicsjaxtransport-networks
  Language:Python 4

• Empoliam / Pottchi

  Cellular Potts Model implemented in C++

  biological-simulationscellular-automatacellular-potts-modelsimulation
  Language:C++ 3

• rwill128 / evo-sim-cuda-python

  An evolution simulation inspired by Biogenesis on Sourceforge.

  biological-simulationsevolutionevolution-strategies
  Language:Jupyter Notebook 3

• Georgelingzj / ecohack-2025

  🎮 A Simulator for Biology Invasion Studies

  biological-simulationsbiologyllmmulti-agents
  Language:Python 2

• gildiamant31 / Computational_Biology-

  Computational Biology Course

  bioinformaticsbiological-simulations
  Language:Python 2

• Neil-Rayu / Genetc-Algo-Sunflower

  This is a simulation of sunfllowers evolution given certain evniormental conditions, it is simulated via a genetic algorthim using a loss/fitness function, corssing over and other biological mechanisms.

  biological-simulationsfitness-functiongenetic-algorithmmachine-learning-algorithmssunflower-simulator
  Language:JavaScript 2

• punamrattu / computational_biophysics

  Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).

  biological-simulationscomputational-biophysicsdata-analysismolecular-dynamicsnanopore
  Language:Shell 2