biology

There are 230 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 5831
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# 3032
openworm / OpenWorm
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
openworm elegans biology simulation
Language:Python 2743
duerrsimon / bioicons
A library of free open source icons for science illustrations in biology and chemistry
biology chemistry graphics illustration science
Language:Vue 1434
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 1058
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 987
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 781
chemicalx
AstraZeneca / chemicalx
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
biology chemistry deep-chemistry deep-learning drug drug-discovery drug-interaction drug-pair geometric-deep-learning geometry graph-neural-network machine-learning pharma polypharmacy pytorch smiles smiles-strings torch torchdrug
Language:Python 730
chainer / chainer-chemistry
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
deep-learning chemistry neural-network biology chainer python graph-convolutional-networks
Language:Python 655
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
550
biojs / biojs
🔬A library of JavaScript components to represent biological data
biojs biology javascript visualisation
497
jvarkit
lindenb / jvarkit
Java utilities for Bioinformatics
bioinformatics java next-generation-sequencing ngs science biology genomics
Language:Java 495
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 470
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 467
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 466
Opentrons / opentrons
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
biology robotics science
Language:Python 439
histolab / histolab
Library for Digital Pathology Image Processing
digital-pathology-data digital-pathology bioinformatics biology wsi hacktoberfest data-science python science-research research pathology
Language:Python 396
awesome-biology
raivivek / awesome-biology
Curated (meta)list of resources for Biology.
biology awesome-list bioinformatics books evolution systems-biology science
368
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 317
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 304
lmdu / pyfastx
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
fasta python biology dna genome assembly sequence fastq bioinformatics
Language:C 276
ropensci / taxize
A taxonomic toolbelt for R
api api-wrapper biodiversity biology darwincore data nomenclature r r-package rstats taxize taxonomy
Language:R 275
BioJulia / Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
bioinformatics biology genomics dna deprecated biojulia biojulia-packages
Language:Julia 264
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
dna igem synthetic-biology vector plasmid rna biology protein
Language:TypeScript 264
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 257
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++ 234
MaayanLab / clustergrammer
An interactive heatmap visualization built using D3.js
clustering visualization python jupyter-notebook jupyter-widget biology heatmap d3
Language:JavaScript 231
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
sandboxels
R74nCom / sandboxels
In-browser falling-sand simulation game with over 500 elements and thousands of reactions.
biology browser-game cellular-automata cellular-automaton chemistry chemistry-lab falling-sand physics-simulation science simulation canvas html5-game javascript javascript-game powder-toy powdertoy sandbox-game simulator simulator-game sandboxels
Language:JavaScript 223
zakandrewking / escher
Build, share, and embed visualizations of metabolic pathways.
javascript escher visualization biology bioinfomatics d3js python
Language:JavaScript 218
keller-mark / awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
awesome-list awesome visualization data-visualization transcriptomics genomics cancer medicine biology
185
pachterlab / poseidon
poseidon system - open source syringe pumps and microscope for laboratories
wetlab open-source-hardware science-research biology
Language:Jupyter Notebook 185
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.
bioinformatics biology computational-biology indra modeling nlp pysb sbml systems-biology
Language:Python 184
SalvatoreRa / tutorial
Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)
machine-learning artificial-intelligence data-science tutorial deep-learning python r bioinformatics biology computer-vision convolutional-neural-networks graph image natural-language-processing nlp streamlit streamlit-webapp tutorials vision-transformer
Language:Jupyter Notebook 181
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 178
wheretrue / biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
arrow bioinformatics biology biopython duckdb polars pyarrow python rust-bio samtools
Language:Rust 175