Find open-source science resources

A python-based workflow manager.

Reinforcement-learning-trained AI agent for treatment reasoning over a universe of 212 biomedical tools, performing multi-step evidence gathering and spawning parallel reasoning branches to reach evidence-grounded clinical decisions (55+ stars, MIT License, 2026)

Biological simulation tools

Differentiable PDE solving framework for machine learning with built-in fluid simulation, supporting PyTorch/JAX/TensorFlow backends and enabling neural network training within physical simulations (TUM, MIT License)

Inflexa is an open-source, agentic orchestration platform for computational biology and translational medicine. It is designed to assist researchers in analyzing multi-omics, cheminformatics, and imaging data by reading published literature, designing multi-step analysis plans, and executing experiments with full reproducibility.

Flow-based generative model for atomistic protein binder design with test-time optimization, SOTA on binder benchmarks (ICLR 2026 Oral, NVIDIA)

First scientific ML benchmark with paired real-world measurements and matched numerical simulations for complex physical systems, featuring 5 scenarios, 700+ trajectories, 10 baseline models, and 9 evaluation metrics with HuggingFace datasets and model checkpoints (Westlake University, CC BY-NC 4.0)

Large-scale knowledge graph and pip-installable client for literature-grounded automated scientific research, connecting papers, authors, institutions, venues, keywords, citations, and a four-level research taxonomy across medicine, social sciences, engineering, computer science, materials science, and more (ZJU NLP, arXiv 2026, 136+ stars, MIT License)

A molecule manipulation library.

AI co-author covering the entire research lifecycle — from an under-specified research direction to a published paper; includes ResearchStudio-Idea for evidence-grounded research ideation and ResearchStudio-Reel for turning finished papers into posters, narrated videos, blogs, and interactive reels; runs as skills on Claude Code and Codex (1.2K+ stars, MIT License, 2026)

LLM-driven machine learning engineering agent using agentic tree search to autonomously draft, debug and benchmark ML code; wins 4× more medals than the best linear agent on OpenAI's MLE-Bench (75 Kaggle competitions) (1.3K+ stars, MIT License)

RFdiffusion is an open source method for structure generation, with or without conditional information (a motif, target etc).

Curated library of 550+ medical research agent skills spanning evidence insights, protocol design, omics/clinical data analysis, and academic writing; each skill is reviewed through MedSkillAudit and compatible with Claude Code, Codex, Open Code, OpenClaw, and SKILL.md-compatible agents (AIPOCH, 1.2K+ stars, MIT License, 2026)

Advanced OCR with PP-StructureV3 document parsing, 13% accuracy improvement, supports 80+ languages

Google Research's hybrid ML/physics atmospheric model combining learned dynamics with physical constraints, outperforming traditional models on 2-15 day forecasts and 40-year climate simulation, developed with ECMWF (Nature 2024)

Py-HLA-Match is a Python library for standardised, rule-based HLA (Human Leukocyte Antigen) matching in retrospective analyses, method development, benchmarking, and in-silico studies in immunogenetics and related fields.

Python package for simulation-based inference enabling likelihood-free Bayesian parameter estimation from scientific simulators, with flexible interfaces for neural posterior estimation, sequential methods, and MCMC/variational backends (Mackelab, 825+ stars)

Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

Pretrained time series foundation model for long-horizon forecasting across diverse scientific domains including climate variables, biomedical signals, and physical observations; decoder-only Transformer architecture with strong zero-shot generalization (19.8K+ stars, Apache 2.0, 2024-2025)

GAIn is a platform for annotating genetic variants, genomic positions, and regions with reproducible, declarative pipelines using curated Genomic Resource Repositories.

atomate2 is a library of computational materials science workflows.

General-purpose biomedical AI agent integrating LLM reasoning with retrieval-augmented planning and code-based execution to autonomously execute diverse biomedical research tasks and generate testable hypotheses (Stanford SNAP, bioRxiv 2025)

Self-evolving AI scientist with 6 specialized sub-agents (plan/research/code/debug/analyze/write) and persistent memory, #1 on DeepResearch Bench II and AstaBench, supporting multi-provider LLMs and multi-channel deployment (Apache 2.0, 2026)

Markerless pose estimation of user-defined features with deep learning for all animals including humans, enabling quantitative behavioral analysis in neuroscience and ethology (Nature Neuroscience 2018, 5.6K+ stars)

ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)

Fully autonomous research from idea to paper with multi-agent debate, citation verification, and OpenClaw integration (11K+ stars, 2026)

High-level open-source geospatial AI package for satellite/aerial imagery analysis, model training, inference, interactive visualization, and QGIS integration, bridging PyTorch/Transformers with remote sensing workflows (MIT, 2026)

Autonomous AI agent for end-to-end spatial proteomics analysis, featuring SP-Bench for agentic multiplexed-imaging workflows (tomtommyyuan, 140+ stars, 2026)

Generalist autonomous research agent that grows a hypothesis tree to optimize any measurable task, beating Claude Code and Codex by 2.5× on the same compute budget across BrowseComp, Terminal-Bench 2.0, math reasoning, and MLE-Bench Lite; supports native CLI, keyless Claude Code/Codex integration, and an MCP tool server (RUC-NLPIR, 866+ stars, Apache 2.0, 2026)

Agricultural machine learning platform

Free-text promptable universal 3D medical image segmentation foundation model enabling zero-shot segmentation of diverse anatomical structures and pathologies via natural language prompts across CT, MRI, and other volumetric imaging modalities (DKFZ, 195+ stars, Apache 2.0)

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Deep learning software to decode EEG, ECG or MEG signals, providing standardized neural network models, preprocessing pipelines, and evaluation workflows for brain-computer interfaces and cognitive neuroscience research (1.2K+ stars, BSD 3-Clause, actively maintained)

SOTA multimodal document parsing with 1.2B parameters outperforming GPT-4o, converts PDFs to LLM-ready Markdown/JSON

Neural network-based cryo-EM heterogeneous reconstruction, modeling continuous 3D structure distributions from single-particle images, with CryoDRGN-ET extending to in-cell cryo-electron tomography (MIT CSAIL, Nature Methods 2021/2024)

Universal machine learning interatomic potential for atomistic simulation of materials, molecules, and biomolecules across the periodic table, with open-source pretrained models and inference tools (Orbital Materials, 2024-2025)

Pythonic Access to the Ensembl database.

Diffusion MR imaging.

From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."

DeepTaxa is a hybrid CNN-BERT deep learning framework for multi-rank taxonomic classification of 16S rRNA gene sequences. It predicts all seven Linnaean ranks from domain to species in a single forward pass and provides pre-trained checkpoints for full-length 16S and V3-V4 amplicons.

A package for creating fast and accurate interatomic potentials.

Learning operators in Fourier space

Google DeepMind's official collection of agentic science skills accelerating scientific workflows with better grounding and higher token efficiency, integrating insights from AlphaGenome, AFDB, UniProt and 30+ other databases and tools (2026)

Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.

An interactive platform that performs statistical analyses on metabolomics datasets and allows visualising results with ease. The interface gives users autonomy in creating figures suited to their reporting and publication needs.

Open-source biomedical AI platform integrating multimodal foundation models (BioMedGPT, PharmolixFM, LangCell) with agentic workflows and 45+ Claude Code skills for drug discovery, protein engineering, and single-cell omics analysis (PharMolix & Tsinghua AIR, 1K+ stars, 2023-2026)

Utilities for working with CSV/Tab-delimited files.

Long-context generative genomic foundation model using 6-mer tokenization for DNA sequence modeling and generation, with v2 model families for prokaryote and eukaryote genomes and pretrained weights available on HuggingFace (GenerTeam, 460+ stars, MIT License, 2025-2026)

Multi-agent system for drug-discovery gene target validation. LangGraph agents over an MCP data layer (~26 data sources, ~44 tools) score evidence across six independent lenses (genetics, biology, safety, clinical, commercial, regulatory) into a provenanced dossier. Configurable local/cloud LLM routing with full Langfuse/OTEL traceability.