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RejuvenationKit is an open-source Python toolkit for reproducible auditing and analysis of longitudinal preclinical rejuvenation studies. It provides protocol-aware missingness checks, experimental-confounding diagnostics, attrition and analysis-readiness profiling, covariance-aware multichannel change detection, sequential response monitoring, randomized longitudinal inference, visualization, and integrity-tracked report bundles.

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)

A compressor of common genomic file formats (BAM, CRAM, FASTQ, VCF etc).

Accessible protein design platform via Google Colab integrating AlphaFold2, RoseTTAFold, and ProteinMPNN for de novo hallucination, fixed backbone design, and binder design (Sergey Ovchinnikov, 2022+)

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

An issue on the UBERON GitHub Issue tracker

Python wrapper for [bedtools](https://github.com/arq5x/bedtools).

Oxford Nanopore's official deep-learning basecaller for nanopore sequencing, converting raw electrical signals into DNA/RNA sequences with integrated modified-base (methylation) detection and efficient CPU/GPU inference; foundational tool for long-read genomics, epigenetics, and real-time sequencing analysis (nanoporetech, 846+ stars, actively maintained)

Turn any AI agent into a life science expert with NVIDIA BioNeMo skills, enabling agentic workflows for drug discovery, protein engineering, and biomolecular design (329+ stars, Apache 2.0 / CC-BY-4.0, 2026)

98B-parameter frontier generative model jointly reasoning over protein sequence, structure, and function, trained on 2.78 billion proteins; generated a novel fluorescent protein (esmGFP) with only 58% sequence identity to known GFPs (EvolutionaryScale, 2024)

Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.

Latent-space probabilistic denoising diffusion model for predicting coarse-grained conformational ensembles of intrinsically disordered proteins and regions from sequence, with GPU/CPU inference, trajectory export, and FAISS-based similarity search (67+ stars, LGPL-3.0)

Machine learning interatomic potentials

Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.

Local-first, open-source AI workbench for scientists — an open alternative to Claude Science (by ai4s-research, maintainers of this list; TypeScript, MIT, 2026)

GenBio AI's software stack for the AI-Driven Digital Organism, supporting adaptation and finetuning of multiscale biological foundation models across DNA, RNA, protein, structure, and single-cell tasks with reproducible CLIs and pretrained model zoo (2025)

Julia differential equations suite

An object-oriented, webGL based JavaScript library for online molecular visualization.

A small language for defining pipeline stages and linking them together to make pipelines.

OpenTFRaw is a standalone, cross-platform reader for Thermo Fisher Scientific .raw mass-spectrometry files, implemented in pure Rust with no dependency on vendor DLLs or .NET. Python bindings built on PyO3 return NumPy arrays for spectral data, straightforward to load into Pandas or Polars. Covers format versions 8 through 66 (LCQ Classic through Orbitrap Astral and modern TSQ instruments), supporting both centroid and profile spectra.

OpenWRaw is a standalone, cross-platform reader for Waters MassLynx .raw acquisition directories, implemented in pure Rust with no dependency on vendor DLLs. Python bindings built on PyO3 expose functions, scans, and ion-mobility data as native Python objects from Waters QTof and SYNAPT instrument families, ready to be assembled into a Pandas or Polars DataFrame.

OpenTimsTDF is a standalone, cross-platform reader for Bruker timsTOF .tdf and .tdf_bin acquisition files, implemented in pure Rust with no dependency on vendor SDKs. Python bindings built on PyO3 expose frame, scan, and peak data as native Python objects, providing ion-mobility-aware access that can be assembled into a Pandas or Polars DataFrame.

Toolkit for large-scale whole-slide image processing supporting 22+ patch encoders (UNI, CONCH, Virchow, H-Optimus-0, etc.), slide encoders (TITAN, GigaPath, PRISM, CHIEF, Madeleine, Feather), tissue segmentation, and multi-GPU inference with end-to-end pipeline and smart resume for standardized deployment of computational pathology foundation models (Mahmood Lab, Harvard Medical School, 553+ stars)

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

The OntoUML Metamodel repository contains the metamodel of the OntoUML language. Unlike the UML profile, this version is independent of UML and presents only the concepts officially supported in the language. This metamodel covers the abstract and concrete syntaxes of the language and serves as the reference for all projects in the OntoUML as a Service (OaaS) ecosystem, including its different model serializations. [from https://github.com/OntoUML/ontouml-metamodel]

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)

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)

the wavefront alignment algorithm (WFA) which expoit sequence similarity to speed up alignment

The Data Privacy Vocabulary provides an ontology (classes and properties) and taxonomies of concepts to represent information regarding how personal data is processed in the form of an ontology or a knowledge graph.

Agent skill for AI-assisted scientific manuscript writing review distilled from Stanford's *Writing in the Sciences* course, performing five sequential editorial audit passes on clarity, voice, structure, consistency, and integrity (2026)

Simulation of large-scale brain models

Simulations of spiking neural networks.

A Python script that converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.

A two-step desktop GUI application for RNA-seq differential gene expression (DEG) analysis. Step 1 reads raw GDC/TCGA STAR gene-count files together with a GDC sample sheet, matches samples to a Tumor/Normal design, and runs PyDESeq2 to produce normalized counts and DEG statistics. Step 2 generates publication-style volcano plots, MA plots, summary bar charts, and expression heatmaps (with optional gene labeling) from the results, exportable as PNG, PDF, SVG, or TIFF. Requires no coding from the user.

Closed-loop multi-agent system from hypothesis to verification across 12 scientific tasks, #1 on MLE-Bench (36.44%)

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)

Machine learning model predicting cellular perturbation response across diverse contexts with State Transition (ST) and State Embedding (SE) variants, featuring CLI tooling, PyPI distribution, and Virtual Cell Challenge integration (575+ stars)

Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard.

First open-source agentic AI physicist turning research questions into structured workflows with rigorous verification and multi-step analytical work for long-horizon physics projects; integrates with Claude Code, Codex, Gemini CLI, and OpenCode (804+ stars, Apache 2.0, 2026)

PinPath enables flexible visualization of (omics) data onto pathways diagrams, allowing users to pinpoint where the relevant changes occur. It supports pathway diagrams from WikiPathways and KEGG, as well as custom GPML and KGML files. Data can be displayed on both native pathway layouts and network representations

JavaScript genome browser that is highly customizable via plugins and track customizations.

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)

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

This package provides panels summarising data points in hexagonal bins for `iSEE`. It is part of `iSEEu`, the iSEE universe of panels that extend the `iSEE` package.

Open software framework for Engineering AI built on transformer building blocks, enabling teams to build, train, and operate industrial simulation models across engineering verticals; includes ready-to-use recipes for CFD (AB-UPT on DrivAerML), external aerodynamics, and heat transfer (234+ stars, ENPL non-commercial license, 2026)

All-atom generative world model for all-to-all biomolecular interaction design, enabling cross-modality generation of proteins, nucleic acids, small molecules, and cyclic peptides with fine-grained epitope-level control and 2-4 orders of magnitude faster design throughput than modality-specific baselines (316+ stars, Apache 2.0)

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)