Repository Index

Theano was a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as PyTensor: www.github.com/pymc-devs/pytensor

An open-source, GPU-accelerated physics simulation engine built upon NVIDIA Warp, specifically targeting roboticists and simulation researchers.

• physics-simulation
• robotics
• nvidia-warp
• newton-physics

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

Eclipse SUMO is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.

• traffic
• simulation
• transport

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

• tensorflow
• deep-neural-network
• genomics
• science

ProtoMotions is a GPU-accelerated simulation and learning framework for training physically simulated digital humans and humanoid robots.

• character-animation
• digital-human
• humanoid
• humanoid-robots

:chart_with_upwards_trend: Adaptive: parallel active learning of mathematical functions

• adaptive-learning
• machine-learning
• python
• live-plots

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Wallet UI simulation tool for BTC, ETH, SOL, XRP, and 200+ assets. Customize displayed balances in a controlled demo environment with persistent visual settings and screenshot-ready previews. Designed for testing, demonstrations, and UI prototyping without altering actual blockchain balances or transactions.

• bitcoin-transaction-tool
• browser-crypto-wallet
• crypto-broadcast-api
• electrum-payment

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

FiPy is a Finite Volume PDE solver written in Python

• scientific-computing
• scientific-computing-with-python
• phase-field
• materials-science

Medical LLM agent and MRI segmentation workspace built on PharmaLLM, with LangGraph, vLLM, and BEU-Net.

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.

• analysis
• claude
• claudecode
• dna

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

Small size matrix handling module with a few linear algebra operations specifically for MicroPython (Python3)

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology