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An EMMO-based domain ontology for atomistic and electronic modelling.

A Python package for protein dynamics analysis

The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries. The main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO).

Vitro is a full stack framework for building semantic web applications. It is not domain specific.

Modular toolchain for an extensible and customizable ETL pipeline that extracts, transforms, and loads clinical data and medical imaging metadata, applying dataset-specific mappings to generate outputs compatible with the EUCAIM Common Data Model (CDM). Its design aims to minimize manual data preparation efforts and facilitate customization and integration with other components, such as data quality assurance tools. Containerized, currently supports input datasets in CSV, JSON, XLSX.

PanAbyss is a tool for exploring and visualizing pangenome graphs. It allows users to search for and display regions of a pangenome using coordinates on a reference individual or based on annotations. It also enables searching for regions associated with a selected set of individuals (for example, those linked to a phenotype), computing proximity trees, and retrieving sequences from a given region.

edfcore is a zero-dependency TypeScript library for reading EDF, EDF+, BDF, and BDF+ physiological recordings in browser and Node.js applications. It provides programmatic access to biosignal samples, channel metadata, per-channel sampling rates, physical units, annotations, and discontinuous recording timelines.

A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.

Open-source image analysis toolkit for high-throughput plant phenotyping, extracting morphological, color, and texture traits from RGB, hyperspectral, and thermal imagery with modular Python workflows for crop improvement, stress detection, and plant biology research (Donald Danforth Plant Science Center, 795+ stars, MPL-2.0)

A transparent, unit-aware calculator for the mathematical relationship between peptide mass, target concentration and solution volume. It normalizes mg, micrograms, mL and microlitres, shows the formula and includes a reference syringe visualization. Research-use-only software: it does not select a solvent, validate a laboratory method, calculate a dose or provide administration guidance.

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

The primary goal of this ontology is to standardize the representation of molecular simulation data, processes, and methodologies across disparate simulation platforms, engines (e.g., GROMACS, AMBER, NAMD), and analysis tools, while ensuring these terms are interoperable with existing life sciences ontologies

Unified Python framework for bulk, single-cell, and spatial RNA-seq multi-omics analysis with deep learning deconvolution (VAE) and graph neural networks, bridging Bindea, Bindea, scanpy and squidpy ecosystems (Nature Communications 2024)

A client to simplify fetching predictions from the Koina web service. Koina is a model repository enabling the remote execution of models. Predictions are generated as a response to HTTP/S requests, the standard protocol used for nearly all web traffic.

Continuously updated functional re-annotation of the Mycobacterium tuberculosis complex gene set, anchored on the MTBC0 ancestral genome rather than on a single strain. Serves one record per gene combining Pfam domains, ESMFold structures with Foldseek search, protein language-model features, orthology, curated knowledge, protein association networks and intra-species selection inferred from 145209 sequenced genomes, with dated sources and a graded confidence level for every field. Intended as a successor to Mycobrowser, which is no longer maintained.

AI-assisted structural engineering workspace for AEC workflows: natural language to structural model, analysis, code-check, and report (171+ stars, MIT License, 2026)

Simple and accurate de novo protein binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta for automated binder discovery (bioRxiv 2024)

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

OpenProteo is the open-source Rust stack for proteomics raw-file access. It reads Thermo, Bruker, and Waters acquisitions through a single API (via the sibling OpenTFRaw, OpenTimsTDF, and OpenWRaw readers), converts them to PSI-MS mzML 1.1.0 with a canonical writer, and provides a zero-copy read_arrow() API (enabled by default) that loads directly into Polars or Pandas via PyArrow. No vendor SDKs, no Windows-only DLLs, no binary blobs in the release pipeline. Includes a one-shot vendor2mzml CLI.

The System Package Data Exchange™ (SPDX®) specification is an open standard designed to represent systems containing software components as Software Bill of Materials (SBOMs). Additionally, SPDX supports AI, data, and security references, making it suitable for a wide range of risk management use cases. This _spdx3_ prefix is for SPDX 3.x versions. For earlier versions, use _spdx.term_.

GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio.

Satellite-powered agricultural and land analytics platform combining Sentinel-2 imagery, Google Earth Engine processing, real-time weather data, soil science databases, and AI-driven crop planning into a unified web dashboard (145+ stars, AGPL-3.0, 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)

Local Python sequence utilities for nucleotide composition, DNA and RNA reverse complements, NCBI genetic-code translation, six-frame candidate ORF enumeration, and IUPAC motif searches. Computase accepts raw nucleotide strings or one FASTA record and returns structured, bounded results with explicit scientific conventions.

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)

Machine learning in Julia

Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.

PathForge is a modular benchmarking framework for multiple instance learning in computational pathology. It supports whole slide image feature extraction, HDF5 artifact generation, tile overviews, benchmarking, pipeline optimization, classification, regression, survival and retrieval tasks, and support for model inference and visualization.

Molecular dynamics analysis

Biomedical Model Context Protocol (MCP) server unifying literature search across PubMed/Europe PMC, entity pivoting across genes/variants/drugs/diseases/pathways/proteins, local study analytics, and Claude Code/Codex integration for agentic biomedical research (531+ stars, MIT License, 2025-2026)

Open-source 3D architectural editor with an AI design assistant; build floor plans with walls, doors, windows, and furniture using natural language, with real-time WebGPU-powered previews (TangSY, 59+ stars, MIT License, 2026)

A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces.

Research agent system deeply integrated with Zotero supporting Agent Mode, skills, multi-model backends (OpenAI-compatible, Claude Code, WebChat, Codex), and MinerU PDF parsing for literature Q&A, summarization, figure inspection, and source comparison (1.3K+ stars, 2026)

Machine learning software for extracting structured metadata from scholarly documents

Local-first, open-source healthcare AI toolkit for clinical NLP and PHI/PII de-identification across 12 languages, running entirely on-device with 1,000+ specialized medical models; provides Python SDK, REST API, Docker deployment, and native Swift apps via OpenMedKit with Apple MLX/CoreML acceleration, supporting HIPAA-aware de-identification with 247 PII checkpoints (3K+ stars, Apache 2.0, arXiv 2508.01630)

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

Deep learning library for Chemistry based on Tensorflow

Open-source bioimage analysis platform for digital pathology and research, featuring AI-powered cell detection, tissue classification, and whole-slide image analysis with extensible scripting and plugin architecture (1.3K+ stars, actively maintained)

Probabilistic programming

ImageArray provides a framework for on-disk and in-memory image arrays, specifically for pyramidal images stored in HDF5, Zarr and life sciences image file formats (OME Bio-Formats).

A comprehensive toolkit that bridges popular Python-based immune repertoire analysis tools and Hugging Face protein language models into the R environment. Provides unified interfaces for TCR distance calculations (tcrdist3), sequence generation probability (OLGA), selection inference (soNNia), clustering (clusTCR), protein embeddings (ESM-2), metaclone discovery (metaclonotypist). Fully compatible with the scRepertoire and immApex ecosystem for single-cell immune repertoire analysis.

This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.

Unified framework for state-of-the-art pre-trained bio foundation models across genomics and transcriptomics, providing standardized interfaces and pipelines for DNA, RNA, and single-cell models including Evo 2, Geneformer, scGPT, and UCE with streamlined inference, benchmarking, and fine-tuning workflows (213+ stars, 2024-2025)

The information resource registry is a listing of data sources present in the NCATS Data Translator system. Each information resource has an identifier, a short description, and a URL to more information about that resource.

Curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines, enabling reproducible social science research with AI agents (Stanford REAP & CoPaper.AI, 1.1K+ stars, 2026)

Human-centered research OS with terminal-first harness and local browser Studio, turning research work into reproducible artifact-backed runs through a 9-stage workflow with human approval gates, resume/rollback controls, and venue-aware manuscript packaging (1K+ stars, 2026)

First any-to-any generative foundation model for Earth Observation, enabling unified multimodal understanding and generation across diverse satellite sensors and geospatial tasks through a single architecture (258+ stars)

Shared multimodal AI agent layer for geospatial Python packages (leafmap, geoai, geemap, STAC, NASA Earthdata) and QGIS, exposing geospatial tools to LLMs with structured metadata, confirmation hooks, and support for OpenAI, Anthropic, Google Gemini, Ollama, and more; includes the OpenGeoAgent QGIS plugin (456+ stars, MIT License)