biology

There are 228 repositories under biology topic.

deepchem / deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
biology deep-learning drug-discovery hacktoberfest materials-science quantum-chemistry
Language:Python 5530
Thrive
Revolutionary-Games / Thrive
The main repository for the development of the evolution game Thrive.
biology csharp evolution game godot godot-engine sandbox science simulation strategy thrive
Language:C# 2857
openworm / OpenWorm
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
biology elegans openworm simulation
Language:Python 2689
duerrsimon / bioicons
A library of free open source icons for science illustrations in biology and chemistry
biology chemistry graphics illustration science
Language:Vue 1360
mims-harvard / TDC
Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics
Language:Jupyter Notebook 1018
kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ncbi bioinformatics download-genomes python biology genomics command-line genbank
Language:Python 956
kyegomez / AlphaFold3
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
ai alphafold artificial-intelligence bio biology biology-ai geneml ml
Language:Python 758
chemicalx
AstraZeneca / chemicalx
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
deep-learning pytorch deep-chemistry graph-neural-network drug drug-pair polypharmacy drug-discovery pharma drug-interaction chemistry biology machine-learning torch geometric-deep-learning geometry smiles smiles-strings torchdrug
Language:Python 714
chainer / chainer-chemistry
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
biology chainer chemistry deep-learning graph-convolutional-networks neural-network python
Language:Python 636
dna-3d-engine
pallada-92 / dna-3d-engine
3d engine implementation in DNA code!
3d 3d-engine biology chemical-kinetics chemical-reaction-networks chemical-reactions cube dna in-vitro molecular-biology molecular-programming piperine raymarching real-reactive-programming strand-displacement
548
biojs / biojs
🔬A library of JavaScript components to represent biological data
biojs biology visualisation javascript
491
jvarkit
lindenb / jvarkit
Java utilities for Bioinformatics
bioinformatics java next-generation-sequencing ngs science biology genomics
Language:Java 485
GMOD / jbrowse
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
genomics genome-browser genome-annotation protein-annotation bioinformatics biology
Language:JavaScript 464
SciML / Catalyst.jl
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
differential-equations chemical-reactions reaction-network sde dsl ode gillespie-algorithm biology systems-biology rate-laws sciml scientific-machine-learning systems-biology-simulation julia simulation
Language:Julia 463
reymond-group / smilesDrawer
A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.
biology chemistry data-visualization javascript-library science
Language:JavaScript 446
Opentrons / opentrons
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
biology robotics science
Language:Python 425
histolab / histolab
Library for Digital Pathology Image Processing
bioinformatics biology data-science digital-pathology digital-pathology-data hacktoberfest pathology python research science-research wsi
Language:Python 379
awesome-biology
raivivek / awesome-biology
Curated (meta)list of resources for Biology.
awesome-list bioinformatics biology books evolution science systems-biology
350
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf
Language:Python 311
BioAmp-EXG-Pill
upsidedownlabs / BioAmp-EXG-Pill
BioAmp EXG Pill is a small and elegant Analog Front End (AFE) board for BioPotential signal acquisition.
bioelectronics emg emg-signal biopotential-signals prosthetics prosthetic-design biology bioamp-emg-pill hardware upsidedownlabs lorforlinux ecg eog eeg board bioamp-exg-pill arduino afe
Language:HTML 279
ropensci / taxize
A taxonomic toolbelt for R
taxonomy data api biodiversity biology rstats nomenclature darwincore taxize api-wrapper r r-package
Language:R 269
lmdu / pyfastx
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
assembly bioinformatics biology dna fasta fastq genome python sequence
Language:C 268
BioJulia / Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
bioinformatics biojulia biojulia-packages biology deprecated dna genomics
Language:Julia 261
intermine
intermine / intermine
A powerful open source data warehouse system
data-warehouse java tomcat genomics open-source opensource lgplv3 postgresql clojure clojurescript biology tomcat8 webservices api perl python bioinformatics genetics data-visualisation data-visualization
Language:Java 254
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
biology dna igem plasmid protein rna synthetic-biology vector
Language:TypeScript 246
MaayanLab / clustergrammer
An interactive heatmap visualization built using D3.js
clustering visualization python jupyter-notebook jupyter-widget biology heatmap d3
Language:JavaScript 230
Benjamin-Lee / deep-rules
Ten Quick Tips for Deep Learning in Biology
deep-learning manuscript manubot biology bioinformatics computational-biology machine-learning data-science genomics
Language:HTML 227
rcedgar / muscle
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
algorithms bioinformatics biology nucleotide-alignment protein-alignment protein-structure protein-structure-alignment sequence-clustering sequence-search
Language:C++ 213
zakandrewking / escher
Build, share, and embed visualizations of metabolic pathways.
bioinfomatics biology d3js escher javascript python visualization
Language:JavaScript 210
sandboxels
R74nCom / sandboxels
In-browser falling-sand simulation game with over 500 elements and thousands of reactions.
biology browser-game canvas cellular-automata cellular-automaton chemistry chemistry-lab falling-sand html5-game javascript javascript-game physics-simulation powder-toy powdertoy sandbox-game sandboxels science simulation simulator simulator-game
Language:JavaScript 182
sorgerlab / indra
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
systems-biology modeling biology computational-biology bioinformatics pysb nlp indra sbml
Language:Python 177
seagull
ljvmiranda921 / seagull
A Python Library for Conway's Game of Life
game-of-life conways-game-of-life artificial-life cellular-automata mathematics biology artificial-life-algorithms simulation-framework
Language:Python 176
pachterlab / poseidon
poseidon system - open source syringe pumps and microscope for laboratories
biology open-source-hardware science-research wetlab
Language:Jupyter Notebook 173
keller-mark / awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
awesome awesome-list biology cancer data-visualization genomics medicine transcriptomics visualization
172
PeptoneLtd / dspp-keras
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
protein protein-structure biology biotechnology machine-learning ai tensorflow keras amino-acids polymer dataset database prediction
Language:Python 169
SalvatoreRa / tutorial
Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)
artificial-intelligence bioinformatics biology computer-vision convolutional-neural-networks data-science deep-learning graph image machine-learning natural-language-processing nlp python r streamlit streamlit-webapp tutorial tutorials vision-transformer
Language:Jupyter Notebook 167