Find open-source science resources

RiSPICE (Rice SNP Prioritization Integrating Chromatin Effects) is a computational framework for prioritizing non-coding rice variants by integrating predicted chromatin effects from a fine-tuned DNA language model.

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.

Comprehensive collection of 125+ ready-to-use scientific skill modules for Claude AI across bioinformatics, cheminformatics, clinical research, ML, and materials science

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

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)

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

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)

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.

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science with 140+ ready-to-use skills and 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard (K-Dense-AI, 26K+ stars, 2025)

A package for creating fast and accurate interatomic potentials.

Learning operators in Fourier space

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)

A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more.

Modular Python suite for Neuro-AI research across all modalities, providing efficient data loaders (NeuralSet), curated datasets (NeuralFetch), scalable training (NeuralTrain), and unified benchmarking (NeuralBench) for building and evaluating neuroscience foundation models (Meta FAIR, 270+ stars, MIT License, 2026)

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)

Composite-objective protein design framework integrating Boltz, AlphaFold2, OpenFold3, ProteinMPNN, and ESM via JAX-based gradient optimization over continuous relaxed sequence space for multi-property binder design (319+ stars, MIT License, 2025)

Agent skills (SKILL.md + deterministic tools) for the AI4S workflow — topic exploration, literature survey, runnable experiments, publication-grade papers, and integrity audit, with every citation and number traceable to its source (by ai4s-research, maintainers of this list; MIT, 2026)

Collection of SKILLS.md guiding AI coding agents (Claude Code, OpenAI Codex, Google Gemini, OpenCode, OpenClaw) through common bioinformatics workflows from basic sequence manipulation to advanced analyses such as single-cell RNA-seq and population genetics; evaluated on the Bio-Task Bench dataset (GPTomics, 969+ stars, MIT License, 2026)

Interactive and hardware-agnostic SDK for laboratory automation, enabling programmatic control of liquid handlers, plate readers, and other lab instruments across multiple vendors; foundational infrastructure for self-driving laboratories and AI-driven experimental execution (447+ stars)

Medical time series foundation model pretrained on 454B time points from heterogeneous clinical corpora spanning ICU physiological signals and hospital EHR, with continuous-time rotary positional encoding, frequency-specialized Mixture-of-Experts, and neural ODE extrapolation for zero-shot forecasting across irregular and multimodal temporal health data (Microsoft, 399+ stars, MIT License)

Semi-automated research assistant for academic research and software development, supporting Claude Code, Codex CLI, Kimi Code CLI, and OpenCode across ideation, coding, experiments, writing, and publication (Galaxy-Dawn, 4.5K+ stars, MIT License, 2026)

First agentic LLM for autonomous data science with end-to-end pipeline from data to analyst-grade reports

Hand-curated Snakemake pipelines to combine identifier cross-references from multiple sources across dozens of biomedical types, including anatomical entities, diseases and phenotypes, genes and proteins and many others.

Deep learning with spiking neural networks in Python, providing gradient-based training of SNNs via PyTorch autodifferentiation for brain-inspired computing and neuromorphic research, with online learning capabilities and extensive tutorials (1.9K+ stars, actively maintained)

First bioinformatics-native AI agent skill library enabling local-first, reproducible genomic and population-genetics research workflows built on OpenClaw (871+ stars, MIT License, 2026)

Beyond text-to-slides generation with PPTEval multi-dimensional evaluation (EMNLP 2025)

A benchmark for ML-guided high-throughput materials discovery.

Lightweight Markdown-only skills for autonomous ML research with cross-model review loops, idea discovery, and experiment automation; no framework lock-in, works with Claude Code, Codex, OpenClaw, or any LLM agent (12.8K+ stars, MIT License, 2026)

Multi-LLM consensus framework for automated cell type annotation in single-cell transcriptomics, integrating predictions from 10+ large language models with iterative discussion and uncertainty quantification to reduce single-model biases, achieving up to 95% accuracy without reference datasets; available as CRAN R package and PyPI Python package with Scanpy/Seurat integration (2025)

Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification problems.

Graph neural network interatomic potential package supporting efficient multi-GPU parallel molecular dynamics simulations, enabling large-scale atomistic modeling with machine learning potentials (MDIL-SNU, MIT License)

E(3)-equivariant neural network interatomic potentials achieving DFT accuracy with up to 1000× less training data than invariant models, foundational architecture behind MACE and Allegro (Harvard, MIT, Nature Communications 2022)

RBPBench is a multi-function tool to evaluate CLIP-seq and other related genomic region data using a comprehensive collection of known RNA-binding protein (RBP) binding motifs. RBPBench can be used for a variety of purposes, from RBP motif search (database or user-supplied RBP motifs) in genomic regions, over motif enrichment and co-occurrence analysis, in-depth comparisons over multiple datasets via sequence and genomic annotation statistics, to benchmarking CLIP-seq peak caller methods as well as comparisons across cell types and CLIP-seq protocols. RBPBench supports both sequence and structure motifs, as well as regular expressions (sequence and structure patterns). Moreover, users can easily provide their own motif collections.

University of Cambridge's foundation model for time-series satellite imagery, enabling efficient extraction of temporal patterns from Earth observation for land classification, canopy height prediction, and other remote sensing tasks

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.

Cross-domain foundation model for continuum dynamics trained on 19 physical scenarios spanning 63 variables, featuring adaptive compute via stride modulation and patch jittering for long-run stability (Polymathic AI, 293+ stars, MIT License)

MCP server, CLI, and agent skills for searching and downloading academic papers from multiple open sources (arXiv, PubMed, bioRxiv, Semantic Scholar, OpenAlex, CORE, Europe PMC, etc.) with unified, deduplicated, LLM-friendly retrieval and an OA-first download fallback chain (OpenAGS, 1.9K+ stars, MIT License, 2025)

Create MSP files containing the isotopic patterns for given molecules with given adducts. The tool is based on enviPat and the RforMassSpectrometry toolbox.

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)

Autonomous multi-agent AI scientist that mirrors a PhD workflow: literature review → grounded hypothesis → real ML experiments → self-critique → write-up; features a deterministic harness with frozen-metric scoring, edit allowlists, and a verified registry to make reward-hacking and hallucination impossible, plus 108 unit tests runnable without API keys or GPUs (461+ stars, MIT License, 2026)

Deep learning library for Chemistry based on Tensorflow

Unified Python framework for extracellular electrophysiology, standardizing interfaces to 10+ ML-based spike sorting algorithms including Kilosort for reproducible neural spike sorting workflows (792+ stars, actively maintained)

Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.

Python package for segmenting geospatial data with the Segment Anything Model (SAM), enabling zero-shot object segmentation in satellite and aerial imagery for remote sensing and Earth observation (MIT, 4k+ stars)

Co-create PowerPoint presentations with Generative AI from documents or topics

PyTorch domain library for geospatial deep learning providing standardized datasets, samplers, transforms, and pre-trained models for remote sensing, land cover mapping, and environmental monitoring (Microsoft, 4K+ stars)