Find open-source science resources

Self-hostable scientific claim-verification and literature-review tool combining Semantic Scholar retrieval, bibliometric scoring, and LLM-based evidence synthesis for large-batch validation workflows

Official Jupyter extension with `%%ai` magic commands and sidebar chat assistant, connecting multiple model providers and local inference

Neuro-imaging file formats.

End-to-end composable multi-agent framework for automating OpenFOAM-based CFD simulations from natural language prompts, managing meshing, case setup, execution, error correction, and post-processing; achieves 100% success rate on 110 FoamBench tasks with Claude Opus 4.6 through Architect-Input Writer-Runner-Reviewer agent collaboration with RAG-enhanced generation and MCP tool integration (RPI CSML, 242+ stars, MIT License)

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)

dadi is a bioinformatics tool for inferring demographic history and selection from genetic data using diffusion approximations, offering speed and flexibility in modeling population dynamics. It supports up to three populations with customizable parameters and provides efficient computational performance.

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)

atomate2 is a library of computational materials science workflows.

Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.

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)

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)

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)

Programmatic framework for designing state-switching proteins via backpropagation through compositional design constraints parameterized by structure prediction models; enables de novo design of allosteric regulators and fluorescent biosensors for arbitrary small-molecule analytes (79+ stars, MIT License, ICML 2026)

Simulations of spiking neural networks.

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

Learnable latent embeddings for joint behavioral and neural analysis, enabling consistent and interpretable mapping of neural activity to behavior across modalities, species, and experiments (EPFL & Harvard, 1K+ stars)

High-throughput PubChem client for batch queries with caching, validation, rate-limit-aware retries, and a simple CLI.

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)

First fully open-source model achieving AlphaFold3-level accuracy with 1000x faster binding affinity prediction (MIT)

Vision foundation model for the tree of life, pretrained on diverse biological imagery across taxa for zero-shot species identification, trait extraction, and biodiversity research (Ohio State University Imageomics Institute)

Highly scalable equivariant deep learning interatomic potentials enabling million-atom molecular dynamics simulations with ab initio accuracy, building on E(3)-equivariant architectures for large-scale atomistic modeling (mir-group, MIT License, 480+ stars)

Biological simulation tools

SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as "sssom:mapping_justification" are defined in the sssom namespace.

197 bioinformatics and life science skills for Claude Code and AI agents, achieving 92.0% accuracy on BixBench. Covers RNA-seq, single-cell analysis, drug discovery, proteomics, and more. Powers OmicsHorizon (195+ stars, 2026)

Decentralized self-organizing teams of AI agents for long-running computational scientific experimentation; agents critique each other's proposals before spending compute and share successes/failures to avoid redundant exploration, achieving +8.33% on BioML-Bench, 1.9× faster nanoGPT optimization, and +12.5% on ProteinGym ACE2-Spike (425+ stars, 2026)

Generative foundation model for functional antibody and nanobody design, supporting de novo generation, affinity maturation, inverse design, structure prediction, and humanization (Tencent AI4S, ICLR 2025)

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.

End-to-end autonomous AI research engine that turns an idea into a complete LaTeX paper by dispatching real computational experiments to local GPUs or SLURM clusters, collecting actual results, generating figures/tables, and writing a data-grounded manuscript rather than LLM hallucinations (OpenRaiser, 1.5K+ stars, MIT License, 2026)

SDK & library for AI-driven scientific computing applications

Generalized biological foundation model with unified nucleic acid and protein language, integrating DNA/RNA/protein sequences (Nature Machine Intelligence 2025)

Automates and standardizes ligand preparation for AutoDock Vina.

Simulation of large-scale brain models

Automated cell type annotation tool for single-cell transcriptomics using gradient boosting and logistic regression with reference atlases, enabling standardized classification across datasets (Wellcome Sanger Institute, Nature Biotechnology 2022)

Automate downloading, opening, and parsing DrugBank.

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)

LLM agents for working with the SRA (Sequence Read Archive) and associated bioinformatics databases, enabling natural language querying of high-throughput sequencing data and metadata across genomic repositories (Arc Institute, 169+ stars, 2024-2026)

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

The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes.

DeepMind's neural network for ab-initio quantum chemistry, directly solving the many-electron Schrödinger equation via variational Monte Carlo with antisymmetric wavefunctions, extended to excited states (Phys. Rev. Research 2020, Science 2024)

Biological vision foundation model trained on TreeOfLife-200M, yielding extraordinary accuracy on diverse biological visual tasks including habitat classification and trait prediction despite a narrow training objective (Ohio State University Imageomics Institute)

A package for accessing data from the NIST webbook...

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)

- Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

The Chromosome Ontology is an automatically derived ontology of chromosomes and chromosome parts.

Interaction Fingerprints for protein-ligand complexes and more.

The Simplified Upper Level Ontology (SULO) is ontology with a minimal set of classes and relations to guide the development of a personal health knowledge graph. [from homepage]

Utilities for working with CSV/Tab-delimited files.

Knowledge graph-guided synthetic data generation for LLM fine-tuning, achieving strong performance on scientific QA (GPQA-Diamond) and math reasoning (AIME)

All-atom biomolecular structure prediction for protein-nucleic acid-small molecule-metal ion complexes, enabling accurate modeling of covalent modifications and assemblies beyond proteins (Baker Lab, Science 2024)