biology

There are 226 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 5156
Thrive
Revolutionary-Games / Thrive
The main repository for the development of the evolution game Thrive.
thrive game simulation evolution strategy biology science sandbox csharp godot godot-engine
Language:C# 2617
openworm / OpenWorm
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
openworm elegans biology simulation
Language:Python 2274
duerrsimon / bioicons
A library of free open source icons for science illustrations in biology and chemistry
illustration science biology chemistry graphics
Language:Vue 1190
mims-harvard / TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
machine-learning therapeutics drug-discovery datasets biology chemistry biomedicine bioinformatics cheminformatics deep-learning benchmarks artificial-intelligence precision-medicine medicine biotech
Language:Jupyter Notebook 933
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 893
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 699
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 612
dna-3d-engine
pallada-92 / dna-3d-engine
3d engine implementation in DNA code!
dna piperine strand-displacement chemical-reaction-networks chemical-kinetics chemical-reactions in-vitro molecular-programming molecular-biology biology 3d 3d-engine cube raymarching real-reactive-programming
544
biojs / biojs
🔬A library of JavaScript components to represent biological data
biojs biology visualisation javascript
484
jvarkit
lindenb / jvarkit
Java utilities for Bioinformatics
bioinformatics java next-generation-sequencing ngs science biology genomics
Language:Java 467
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 457
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 423
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 402
Opentrons / opentrons
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
biology robotics science
Language:Python 387
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 340
awesome-biology
raivivek / awesome-biology
Curated (meta)list of resources for Biology.
biology awesome-list bioinformatics books evolution systems-biology science
326
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 307
ropensci / taxize
A taxonomic toolbelt for R
taxonomy data api biodiversity biology rstats nomenclature darwincore taxize api-wrapper r r-package
Language:R 262
BioJulia / Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
bioinformatics biology genomics dna deprecated biojulia biojulia-packages
Language:Julia 261
intermine
intermine / intermine
A powerful open source data warehouse system
api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices
Language:Java 248
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 238
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 237
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
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
dna igem synthetic-biology vector plasmid rna biology protein
Language:TypeScript 217
zakandrewking / escher
Build, share, and embed visualizations of metabolic pathways.
javascript escher visualization biology bioinfomatics d3js python
Language:JavaScript 204
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 172
pachterlab / poseidon
poseidon system - open source syringe pumps and microscope for laboratories
wetlab open-source-hardware science-research biology
Language:Jupyter Notebook 168
PeptoneLtd / dspp-keras
Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.
ai amino-acids biology biotechnology database dataset keras machine-learning polymer prediction protein protein-structure tensorflow
Language:Python 166
rcedgar / muscle
Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.
bioinformatics biology algorithms
Language:C++ 165
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 160
pydna
BjornFJohansson / pydna
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
bioinformatics biopython python anaconda dna gel jupyter-notebooks biology pydna jupyter-notebook gel-simulation jupyter gibson-assembly cloning-strategies gel-electrophoresis assembly-strategies simulation genbank fasta
Language:Jupyter Notebook 155
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
151
BioJulia / BioSequences.jl
Biological sequences for the julia language
biojulia bioinformatics biology biological-sequences
Language:Julia 146
epam / cloud-pipeline
Cloud agnostic genomics analysis, scientific computation and storage platform
aws azure biology chemistry cloud google-cloud modelling ngs
Language:Java 142