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The Top 23 Python Biology Open Source Projects

Open source projects categorized as Python Biology
Categories > Science > Biology
Deepchem ⭐ 4,876
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
dependent packages 8total releases 756most recent commit 3 months agopypi deepchem} Downloads
Openworm ⭐ 2,214
Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
most recent commit 5 months ago
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25most recent commit 9 months agopypi ncbi-genome-download} Downloads
Chemicalx ⭐ 657
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
total releases 10most recent commit 7 months ago
Chainer Chemistry ⭐ 609
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
most recent commit a year ago
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52most recent commit 3 months agopypi biotite} Downloads
Opentrons ⭐ 372
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
dependent packages 6total releases 244most recent commit 3 months agopypi opentrons} Downloads
Histolab ⭐ 315
Library for Digital Pathology Image Processing
total releases 21most recent commit 3 months ago
Provis ⭐ 272
Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."
most recent commit a year ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Clustergrammer ⭐ 228
An interactive heatmap visualization built using D3.js
dependent packages 11total releases 75most recent commit a year agonpm clustergrammer} Downloads
Intermine ⭐ 228
A powerful open source data warehouse system
dependent packages 2total releases 8most recent commit 2 years ago
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68most recent commit 5 months agopypi pyfastx} Downloads
Pypesto ⭐ 183
python Parameter EStimation TOolbox
dependent packages 3total releases 38most recent commit 3 months agopypi pypesto} Downloads
Escher ⭐ 178
Build, share, and embed visualizations of metabolic pathways.
dependent packages 5total releases 31most recent commit a year agonpm escher} Downloads
Indra ⭐ 154
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.
dependent packages 7total releases 29most recent commit 3 months agopypi indra} Downloads
Pysb ⭐ 145
Python framework for Systems Biology modeling
most recent commit 9 months ago
Pydna ⭐ 140
Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
dependent packages 7total releases 110most recent commit 4 months agopypi pydna} Downloads
Seagull ⭐ 120
A Python Library for Conway's Game of Life
total releases 6most recent commit 3 years ago
Aitom ⭐ 114
AI for tomography
most recent commit 5 months ago
Buddysuite ⭐ 105
Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files
total releases 18most recent commit 2 years ago
Python_biologist ⭐ 101
Python Programming for Biologists
most recent commit 7 months ago
Biobear ⭐ 100
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
most recent commit 3 months ago
The 10 Most Depended On Python Biology Open Source Projects
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52latest release September 09, 2023most recent commit 3 months agopypi biotite} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Clustergrammer ⭐ 228
An interactive heatmap visualization built using D3.js
dependent packages 11total releases 75latest release March 14, 2018most recent commit a year agonpm clustergrammer} Downloads
Deepchem ⭐ 4,876
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
dependent packages 8total releases 756latest release December 08, 2023most recent commit 3 months agopypi deepchem} Downloads
Opentrons ⭐ 372
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
dependent packages 6total releases 244latest release December 11, 2023most recent commit 3 months agopypi opentrons} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25latest release July 28, 2023most recent commit 9 months agopypi ncbi-genome-download} Downloads
Clustergrammer2 ⭐ 99
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
dependent packages 5total releases 67latest release July 18, 2021most recent commit 2 years agonpm clustergrammer2} Downloads
Escher ⭐ 178
Build, share, and embed visualizations of metabolic pathways.
dependent packages 5total releases 31latest release September 05, 2019most recent commit a year agonpm escher} Downloads
The 10 Latest Releases In Python Biology Open Source Projects
Opentrons ⭐ 372
Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2
dependent packages 6total releases 244latest release December 11, 2023most recent commit 3 months agopypi opentrons} Downloads
Deepchem ⭐ 4,876
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
dependent packages 8total releases 756latest release December 08, 2023most recent commit 3 months agopypi deepchem} Downloads
Pypesto ⭐ 183
python Parameter EStimation TOolbox
dependent packages 3total releases 38latest release December 06, 2023most recent commit 3 months agopypi pypesto} Downloads
Bluecellulab ⭐ 8
Simulating and experimenting on single neurons
dependent packages 1total releases 54latest release December 05, 2023most recent commit 4 months agopypi bluecellulab} Downloads
Pioreactor ⭐ 75
Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
total releases 27latest release November 29, 2023most recent commit 3 months ago
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Qpcr ⭐ 12
A python package to analyse qPCR data for single-use or high-throughput application
total releases 12latest release October 31, 2023most recent commit 6 months ago
Cogent3 ⭐ 79
Comparative Genomics Toolkit 3
dependent packages 2total releases 18latest release September 22, 2023most recent commit 3 months agopypi cogent3} Downloads
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