List of Computer Science courses with video lectures.

A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Protein Graph Library

SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

WebGL accelerated JavaScript molecular graphics library

A comprehensive library for computational molecular biology

A list of schools and researchers in computational neuroscience

Working with molecular structures in pandas DataFrames

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

A Go package for engineering organisms.

A high-performance, Pythonic language for bioinformatics

Interactive network visualization in Python and Dash, powered by Cytoscape.js

A publicly-editable collection of open computational neuroscience resources

Cell type annotation for single-cell RNA-seq using multi-LLM consensus

COBRApy is a package for constraint-based modeling of metabolic networks.

Implementation of GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation (ICLR 2022).

Official repository for the ProteinGym benchmarks

DANCE: a deep learning library and benchmark platform for single-cell analysis

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25

Spatial alignment of single cell transcriptomic data.

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

Syntax highlighting for computational biology

UCSC Genome Browser source. "beta" is released version / "master" is testing.

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Next generation sequencing reads de novo assembler.

A geometry-complete diffusion generative model (GCDM) for 3D molecule generation and optimization. (Nature CommsChem)

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)