Biology Open Source Projects

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

The main repository for the development of the evolution game Thrive.

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

A list of deep learning implementations in biology

A curated list of awesome deep learning applications in the field of computational biology

A library of free open source icons for science illustrations in biology and chemistry

resources for learning bioinformatics

Unix, R and python tools for genomics and data science

Therapeutics Commons (TDC): Multimodal Foundation for Therapeutic Science

Scripts to download genomes from the NCBI FTP servers

A comprehensive library for computational molecular biology

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

A curated list of amazingly awesome articles, websites and resources about diversity in technology.

A small, highly performant JavaScript component for parsing and drawing SMILES strings. Released under the MIT license.

3d engine implementation in DNA code!

Awesome Blogs

Java utilities for Bioinformatics

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

🔬A library of JavaScript components to represent biological data

Application of formal systems to model biological systems

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Library for Digital Pathology Image Processing

Curated (meta)list of resources for Biology.

In-browser falling-sand simulation game with over 500 elements and thousands of reactions.

BioAmp EXG Pill is a small and elegant Analog Front End (AFE) board for BioPotential signal acquisition.

Community-provided extensions to Seurat

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

a JavaScript DNA, RNA, and protein sequence viewer

🔬 A repository of resources related to citizen, community-based and/or non-institutional science

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

A taxonomic toolbelt for R

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

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.

python Parameter EStimation TOolbox

Syntax highlighting for computational biology

A powerful open source data warehouse system

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

An interactive heatmap visualization built using D3.js

A list of web-based interactive biological data visualizations.

poseidon system - open source syringe pumps and microscope for laboratories

Please use opencobra/escher for current Escher development. That repository is the preferred home for the latest community-maintained version of Escher and is aligned with the npm package, PyPI package, and website deployments.

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Ten Quick Tips for Deep Learning in Biology

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

Computational biology and medical image processing scripts and programs

A curated list of Synthetic Biology / Genetic Engineering projects, articles and resources. The main idea is that everyone can contribute here, so we can have a central repository of informations about this fascinating subject that we all can keep up-to-date.

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.

Literature of deep learning for graphs in Chemistry and Biology

Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Python framework for Systems Biology modeling

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

A place to collect papers that are related to deep learning and computational biology

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

A Python Library for Conway's Game of Life

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

Main documentation site for NRNB GSoC project ideas and resources