Repository Index

Count your code, quickly.

• tokei
• cloc
• badge
• rust

Open source code for AlphaFold 2.

Suite of tools for deploying and training deep learning models using the JVM. Highlights include model import for keras, tensorflow, and onnx/pytorch, a modular and tiny c++ library for running math code and a java based math library on top of the core c++ library. Also includes samediff: a pytorch/tensorflow like library for running deep learn...

• java
• gpu
• deeplearning
• neural-nets

Sloc, Cloc and Code: scc is a very fast accurate code counter with complexity calculations and COCOMO estimates written in pure Go

• sloccount
• cloc
• complexity
• tokei

Efficiently computes derivatives of NumPy code.

• autograd
• automatic-differentiation
• numpy
• python

A fast and flexible implementation of Rigid Body Dynamics algorithms and their analytical derivatives

• robotics
• dynamics
• analytical-derivatives
• kinematics

Code for running RFdiffusion

CasADi is a symbolic framework for numeric optimization implementing automatic differentiation in forward and reverse modes on sparse matrix-valued computational graphs. It supports self-contained C-code generation and interfaces state-of-the-art codes such as SUNDIALS, IPOPT etc. It can be used from C++, Python, Matlab/Octave, Julia or Javascript

• optimization
• nonlinear
• derivatives
• code-generation

Source code of PyGAD, a Python 3 library for building the genetic algorithm and training machine learning algorithms (Keras & PyTorch).

• python
• genetic-algorithm
• optimization
• numpy

Weather in terminal, with ANSI colors and Unicode symbols

• weather
• terminal
• ansi
• unicode

Code for the ProteinMPNN paper

Unknown Horizons official code repository

• game
• python
• strategy
• simulation

Geo-related tools PHP 7.3+ library built atop Geocoder and React libraries

• php
• geolocation
• geotools
• geo

Brian is a free, open source simulator for spiking neural networks.

• python
• neuroscience
• science
• differential-equations

A coupling library and ecosystem for partitioned multi-physics and multi-scale simulations, including surface and volume coupling.

• multi-physics
• fluid-structure-interaction
• high-performance-computing
• conjugate-heat-transfer

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

HARFANG 3D source code public repository

• 3d
• realtime
• cpp
• vr

The Chemistry Development Kit

• code4lib
• chemistry
• java
• cheminformatics

Universal SKILL.md catalog for research workflows: literature review, research design, project memory, manuscript writing, and cross-agent delegation for Claude Code, Codex, Gemini, Cursor, OpenClaw, and generic AI clients.

• academic-writing
• ai-skills
• notebooklm
• obsidian

Object detection system using deformable part models (DPMs) and latent SVM (voc-release5). You may want to use the latest tarball on my website. The github code may include code changes that have not been tested as thoroughly and will not necessarily reproduce the results on the website.

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)

Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs

• gpu
• exascale
• cfd
• fortran

Privacy-friendly, open-source analytics for WordPress — GDPR compliant, cookieless, and fast

• analytics
• privacy
• wordpress
• google-analytics