Find open-source science resources

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)

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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

# DrugGen 2: A disease-aware language model for enhancing drug discovery DrugGen-2 is a disease‑aware language model specialized for generating drug-like SMILES structures based on both disease pathways and protein sequence.

CENO-P-1B is the multi-species alignment (MSA) post-trained variant of the 1B CENO DNA foundation model, for variant effect prediction (VEP). It carries intraencodingpattern in its config and ships the MSA scoring path (modelingcenop.py), which consumes a per-token seq_idx to score packed MSA…

CENO-1B-131k is the long-context (131k) checkpoint of the 1B CENO DNA foundation model — a causal language model over genomic sequence built on a Nemotron-H Mamba / Attention / Mixture-of-Experts hybrid backbone (no MSA inputs).

CENO-80M-1m is the long-context (1M) checkpoint of the 80M CENO DNA foundation model — a causal language model over genomic sequence built on a Nemotron-H Mamba / Attention / Mixture-of-Experts hybrid backbone (no MSA inputs).

Plain-text, git-tracked electronic lab notebook (ELN) for reproducible bioinformatics — threads your R & Python figures into living lab notes with full provenance. Built for single-cell / CyTOF / flow cytometry; works with Obsidian, Quarto & Jupyter.

World's first fully open, accelerated weather AI software stack with Medium Range forecasting and Nowcasting models using generative AI (January 2026)

Fast, interactive, multi-dimensional image viewer for Python, foundational platform for scientific imaging AI with a rich plugin ecosystem integrating deep learning segmentation, object tracking, and microscopy analysis workflows (2.6K+ stars)

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)

💻 Github | 📄 Report (Coming soon...) | 🚀 Demo

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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."

A 1.7B-parameter causal language model distilled from Qwen3-30B-A3B on 6,122 STEM chain-of-thought samples using discrepancy-informed knowledge distillation. The training objective emphasizes proof structure, detects reasoning pivot tokens through token-level divergence dynamics, smooths…

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.

Next-generation benchmark for data-driven global weather models with standardized evaluation framework and curated datasets for ML forecasting (Google Research, 2024)

Fine-tuned ESM-2 650M with LoRA for predicting protein subcellular localization (10 classes).

PhenoVisionL is a Vision Transformer (ViT-Large) model fine-tuned to detect leaf phenological states in plant photographs: green leaves, colored (senescent) leaves, and breaking leaf buds. It was trained on 165,988 iNaturalist records of deciduous woody plants using a two-stage semi-supervised…

PhenoVision is a Vision Transformer (ViT-Large) model fine-tuned to detect flowers and fruits in plant photographs. It was trained on 1.5 million human-annotated iNaturalist images and has been used to generate over 30 million new phenology records across 119,000+ plant species, vastly expanding…

> NEXUS domain specialist for medical Q&A and clinical reasoning — lightweight & uncensored.

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.

Deep learning-based bioacoustic monitoring framework for automated bird species identification from audio recordings, supporting 6,000+ species globally with real-time analysis, batch processing, and API deployment; foundational tool in biodiversity research, conservation biology, and ecological acoustic monitoring (Cornell Lab of Ornithology, 1.5K+ stars, MIT License)