biosimulations/biosimulations

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

Language: TypeScript - Size: 198 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 41 - Forks: 14

blue-lotus-org/neology-life

Generate a unique lifeform concept based on the user-provided specifications and `hydrogen` as the primary element, without relying on existing biological knowledge.

Language: TypeScript - Size: 129 KB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 0 - Forks: 0

PMEAL/pytrax

Random walk to calculate the tortuosity tensor of images

Language: Python - Size: 94.7 KB - Last synced at: 6 days ago - Pushed at: almost 2 years ago - Stars: 29 - Forks: 18

brian-team/brian2

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

Language: Python - Size: 35.9 MB - Last synced at: 8 days ago - Pushed at: 10 days ago - Stars: 996 - Forks: 237

SuzanneMondal/TGFb-Network-Boolean-Dynamic-Modelling

This is a collection of programs written to achieve various outcomes based on the boolean dynamic simulation of a 6-node Transforming Growth Factor-β (TGFβ) signaling network

Size: 24.4 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 0 - Forks: 0

opensim-org/opensim-core

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

Language: C++ - Size: 209 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 850 - Forks: 331

DamCB/tyssue

An epithelium simulation library

Language: Python - Size: 56.2 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 61 - Forks: 21

NullPointerExcy/Extended_LIF_Neurons

This repository presents an advanced LIF neuron model with dynamic spike probability, adaptive thresholds, synaptic plasticity, and neuromodulation for more biologically realistic behavior. Key features include membrane potential tracking, stochastic and deterministic spike generation, adaptive excitability, and PyTorch integration.

Language: Python - Size: 2.7 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

PascalCorpsman/biosim4_FPC_translation Fork of davidrmiller/biosim4

Biological evolution simulator

Language: Pascal - Size: 118 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 7 - Forks: 0

brian-team/brian2cuda

A brian2 extension to simulate spiking neural networks on GPUs

Language: Python - Size: 122 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 63 - Forks: 13

Edinburgh-Genome-Foundry/kappagate

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

Language: Python - Size: 257 KB - Last synced at: 20 days ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 0

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++ - Size: 6.01 MB - Last synced at: 18 days ago - Pushed at: over 5 years ago - Stars: 135 - Forks: 23

BlueBrain/BluePyOpt 📦

Blue Brain Python Optimisation Library

Language: Python - Size: 57.5 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 211 - Forks: 100

kiwijuice56/evolution-simulation

Interactive game to simulate emergence and natural selection in biological systems

Language: Java - Size: 582 KB - Last synced at: 7 days ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 0

briandconnelly/hankshaweffect 📦

Model, Data, and Analysis Scripts for "The Evolution of Cooperation by the Hankshaw Effect"

Language: Python - Size: 314 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 2

Georgelingzj/ecohack-2025

🎮 A Simulator for Biology Invasion Studies

Language: Python - Size: 1.92 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

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 - Size: 168 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 6

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.

Language: Python - Size: 1.83 MB - Last synced at: 5 days ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0

motexture/Genesis

Mimic the behaviors of biological neurons using pytorch

Language: Python - Size: 37.1 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

ryarazi/PTMC.jl

PTMC.jl (Photon Transport Monte Carlo) is a Julia code based on the Monte Carlo modeling of photon transport in multi-layered tissues (MCML) algorithm.

Language: Julia - Size: 31.3 KB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

rileyjshaw/terra

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

Language: JavaScript - Size: 373 KB - Last synced at: 7 months ago - Pushed at: over 5 years ago - Stars: 610 - Forks: 46

sourceduty/Biological_Reactor

☣️ Specialized biological simulation and research assistant. The first and original AI-Assisted Computational Reactor.

Size: 3.91 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

BharadwajMahanthi/Quantbiologicalwithml

This project was developed as a personal research project after my Master's degree. It aims to explore the intersection of quantum biology and the effects of radiation on fungal species, leveraging advanced data analysis and simulation techniques.

Language: Jupyter Notebook - Size: 6.18 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

BrosnanYuen/RayBNN_Cell

Cell Position Generator for RayBNN

Language: Rust - Size: 109 KB - Last synced at: 6 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

MindTheGap-ERC/CarbonateStratPalEvo

Code for "Identification of the Mode of Evolution in Incomplete Carbonate Successions"

Language: R - Size: 231 MB - Last synced at: 8 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

Axelwickm/NeuroCorrelation

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

Language: C++ - Size: 1.63 MB - Last synced at: 9 months ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 1

Abhishake-Patel/Modelling-and-Optimization-in-Molecular-and-Biological-Networks

Modelling and Optimization of Models with a focus on Healthcare and Biological Networks

Language: HTML - Size: 8.09 MB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

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.

Language: Python - Size: 26.4 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 2

trfore/chatmodel

Neuronal Simulation of the Granule Cell Layer within the Cerebellar Cortex

Language: Python - Size: 26.1 MB - Last synced at: 23 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 1

tbersez/netlogo_proj

Partern formation in discrete time & space model

Language: NetLogo - Size: 70.3 KB - Last synced at: 12 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

guilherme-marcello/karyogapy

Generator of chromosome sets based on the scientific concepts of human embryonic organism formation

Language: Python - Size: 12.7 KB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

Linux-cpp-lisp/navigation-by-deja-vu

Simulation of the navigation-by-scene-familiarity mechanism with a local sensor

Language: Python - Size: 3.28 MB - Last synced at: about 2 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

laurentperrinet/2019-04-03_a_course_on_vision_and_modelization

cours VLC

Language: HTML - Size: 101 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 0

pchlenski/misdeed

Microbiome data simulator for power analysis

Language: Jupyter Notebook - Size: 23.5 MB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

briandconnelly/nicheconstruct

Model, Data, and Analysis for "Negative Niche Construction Favors the Evolution of Cooperation"

Language: TeX - Size: 496 MB - Last synced at: about 1 year ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 0

v--/neuronsim

A Hodgkin-Huxley model visualization for a neural tree

Language: D - Size: 4.18 MB - Last synced at: 12 months ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 1

brainpy/examples

Examples of BrainPy

Language: Jupyter Notebook - Size: 113 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 7

bio-phys/BioEn

BioEn - Bayesian Inference Of ENsembles

Language: Python - Size: 47.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 5

kernelshreyak/livmach

An organism simulation framework based on cell growth and resultant emergent phenomena.

Language: C++ - Size: 16.6 KB - Last synced at: 21 days ago - Pushed at: over 8 years ago - Stars: 2 - Forks: 0

AidenKerr/genetic-v2

Genetic Algorithm that simulates natural selection & evolution visually with a custom-built algorithm

Language: JavaScript - Size: 1.41 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

artainmo/physarum_polycephalum-simulation

Personal project. Visual simulation of an intelligent slime-mold, a biological form of intelligence without a nervous system.

Language: JavaScript - Size: 54.7 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

newmanjb/DigestiveSystem

Biological simulation of the digestive system written in python.

Language: Python - Size: 39.1 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

Host-pathogen-evol/Genome-Size-Evolution-Project

HOME OF THE 2-SPEED GENOME MODEL

Language: Jupyter Notebook - Size: 27.7 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 2

punamrattu/computational_biophysics

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

Language: Shell - Size: 20.5 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

tzeitim/genome-blender

Scripts to create cartoons of 3D genomes

Language: Python - Size: 5.07 MB - Last synced at: 5 days ago - Pushed at: about 1 year ago - Stars: 13 - Forks: 5

nilot-pal/Blood-flow-into-tumor

Tracking Multiphase blood flow into a tumor

Language: C - Size: 1.04 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

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.

Language: JavaScript - Size: 138 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

gildiamant31/Computational_Biology-

Computational Biology Course

Language: Python - Size: 122 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0

roman-komac/NPMP_BIO

NPMP 2017/18 - BIO seminar D master-slave flip-flop

Language: Java - Size: 6.5 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

jsutlive/Cell-Mechanics-Simulator

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

Language: Java - Size: 15.4 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

ali-ramadhan/lagrangian-microbes

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

Language: Python - Size: 2.37 MB - Last synced at: 11 days ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 0

rwill128/evo-sim-cuda-python

An evolution simulation inspired by Biogenesis on Sourceforge.

Language: Jupyter Notebook - Size: 1.55 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 0

melimat/Populations

Simple console aplication for simulating grownig of populations in biology

Language: Python - Size: 9.77 KB - Last synced at: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

BjornFJohansson/ypkpathway

Automatic pathway assembly with the YeastPathwayKit

Language: Python - Size: 37.1 MB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1

souvik1982/Brain

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

Language: C++ - Size: 387 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 13 - Forks: 5

Waximilian/PhefluxTools

PhefluxTools is a comprehensive Python library that offers a wide range of functions and utilities to simplify common computational tasks. It provides a collection of powerful tools for data manipulation, file handling, statistical analysis, visualization, and integration with computational biology.

Language: Python - Size: 10.7 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

alex-rigos/Community-Enforcement

A project on how third-party enforcement systems that sustain cooperation can emerge evolutionarily

Language: Julia - Size: 89.6 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

LS-2ednar/OpenFOAM_Programming

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

Language: C++ - Size: 53.7 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 0

programandoconro/Simulaciones-de-epidemias

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

Language: R - Size: 196 KB - Last synced at: 14 days ago - Pushed at: about 5 years ago - Stars: 6 - Forks: 4

Empoliam/Pottchi

Cellular Potts Model implemented in C++

Language: C++ - Size: 909 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

RayPops/Cancer-Spread-Simulation

A simulation of complex microorganisms such as Mycoplasma, Staphylococcus Aureus, Lactobacillus and their interaction with a cancerous cell.

Language: Java - Size: 9.06 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

KeepFloyding/OpenFOAM-phys-flow

Openfoam library for physiological flow. Solvers and boundary conditions.

Language: C++ - Size: 1.66 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 10 - Forks: 8

lillux/gillespie_ssa

Implementation of Gillespie Stochastic Simulation Algorithm

Language: Jupyter Notebook - Size: 495 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

newmanjb/TheBody

An object-oriented model of the workings of the human body written in java and scala

Language: Java - Size: 166 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

trihedral/Blobolution

An environment programmed to train Artificial Neural Networks (ANNs) through simulated natural selection (genetic algorithm). Numerous objects with independent ANNs interact with each other, competing for simulated limited resources.

Language: Java - Size: 1.1 MB - Last synced at: 13 days ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

siantonelli/ModelsTranslator

Bachelor's thesis project: A phml-to-modelica translation tool for biological models

Language: C++ - Size: 46.9 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

OMR5221/ProteinSynth

Protein Synthesis Project Using Python, BioPython, and BioSQL

Language: Python - Size: 223 KB - Last synced at: 30 days ago - Pushed at: about 10 years ago - Stars: 1 - Forks: 0

pbentkowski/MHC_Evolution

Evolution of the major histocompatibility complex genes repertoire and number of copies in an agent-based modelling approach

Language: C++ - Size: 46.8 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

sepehrmn/nest-simulator Fork of nest/nest-simulator

Sepehr's fork - check branches for original contributions and ongoing work

Language: C++ - Size: 140 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Edinburgh-Genome-Foundry/topkappy

:waxing_gibbous_moon: Pythonic bindings for the Kappa model simulation language

Language: Python - Size: 6.95 MB - Last synced at: 12 months ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

bharathananth/models_for_teaching

Shiny apps to teach simple dynamical models in biology with an emphasis on oscillations

Language: R - Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 1

Luke-Jacobs/Population-Evolution-Simulator

A simulation of biological evolution using selection by traits caused by environmental factors. Shows an example of Hardy-Weinberg equilibrium. For AP Bio extra credit!

Language: Python - Size: 735 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

krkvis/biosim_g20_ida_kjersti Fork of idaln/biosim_g20_ida_kjersti

The project of group 20 for the course INF200 Advanced Programming in January 2020.

Size: 2.25 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

amandachen1024/Glycolysis-Model

Language: Component Pascal - Size: 37.1 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Lysferd/ubiquitous-computing-machine

Ventricular Tissue Simulator

Language: C++ - Size: 37.1 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

raviq/Mice

random walking mice

Language: C++ - Size: 54.7 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

hakimbazol/iGEMITB2017

The codes of Drylab Team, iGEM ITB 2017 to support the wetlab.

Language: MATLAB - Size: 2.93 KB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

JiangXL/SystemBioCode

Code of system biology class

Language: MATLAB - Size: 17.3 MB - Last synced at: 4 days ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

melnyashka/horizontal_gene_transfer

Cemracs 2018 project (CIRM, July-August 2018)

Language: Python - Size: 112 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

sima15/VascularNetworkOptimization

To find out more about this project, checkout my website!

Language: TeX - Size: 49.4 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

amirmasoudabdol/flyOpt

The Drosophila melanogaster gap genes circuit simulator, coupled with Scatter Search optimization algorithm

Language: C - Size: 524 KB - Last synced at: about 2 months ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

Oliver-Binns/PRIY

Project on agent-based simulations for the GPU. My final year dissertation project co-supervised by Fiona Polack (Keele University) and Kieran Alden (University of York) with additional support provided by Richard Paige (UoY).

Language: TeX - Size: 29.6 MB - Last synced at: 5 months ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

dominicrutk/Biology-Project

Language: Java - Size: 23.4 KB - Last synced at: 14 days ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

widdowquinn/SI_Pritchard_Birch_2014

Supplementary information/data for Pritchard & Birch (2014) doi:10.1111/mpp.12210

Language: Component Pascal - Size: 1020 KB - Last synced at: about 1 month ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

qnighy/kappa.vim

Vim syntax for Kappa executable knowledge simulator

Language: VimL - Size: 1.95 KB - Last synced at: 7 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

anne27/Quantitative-Biology

Simulations for apoptosis analysis relevant to Quantitative Biology.

Language: Python - Size: 980 KB - Last synced at: 10 months ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1

StarGate01/LSystemTree_WebGL

Random trees created using a 3D sprite-based L-system

Language: JavaScript - Size: 2.09 MB - Last synced at: 10 days ago - Pushed at: about 10 years ago - Stars: 0 - Forks: 0

arinbjornk/DNAsupercoil

A model of a DNA supercoiling insulator in a transcription-translation system

Language: Matlab - Size: 240 KB - Last synced at: 3 days ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

akostajti/genetransformations

A simple python web application modeling certain kind of gene transformations

Language: Python - Size: 1.09 MB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

tirtharajdash/DORAEMON

Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

briandconnelly/resource-biofilm

Model, configuration, data, analysis, and figures for Resource Abundance and the Critical Transition to Cooperation

Language: R - Size: 143 MB - Last synced at: about 2 years ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0