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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.

BRANCHSNV reports strict clade-exclusive nucleotide markers separately from single-nucleotide substitutions reconstructed on a selected edge of a rooted phylogenetic tree, while retaining ambiguity across equally parsimonious ancestral-state reconstructions.

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)

Deterministic, rule-based variant interpretation platform for clinical genetics laboratories. Automates ACMG/AMP 2015 classification using a Bayesian point-based framework (Tavtigian et al. 2018) with BayesDel ClinGen SVI-calibrated thresholds (Pejaver et al. 2022). Integrates 8 reference databases (gnomAD v4.1, ClinVar, dbNSFP 4.9c, SpliceAI, gnomAD Constraint, HPO, ClinGen, Ensembl VEP). Analyzes nuclear and mtDNA variants, structural and copy-number variants (SV/CNV), with trio/family and cohort analysis. Supports HPO-based phenotype matching, biomedical literature mining across 2M+ PubMed publications, and structured clinical report generation. AI assists in evidence synthesis but does not make classification decisions. EU-hosted on dedicated infrastructure in Helsinki, Finland (GDPR-compliant).

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.

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 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

BondShift: Organic Mechanism Reasoning

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)

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_.

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)

Molecular dynamics analysis

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)

Probabilistic programming

A clinical reasoning assistant for early-stage Alzheimer's assessment. It joins a 3D MRI + biomarker classifier (Vbai-2.6AD) to a reasoning LLM (Gemma 4 12B) inside a single forward pass — the diagnosis is passed as vectors, not text.

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.

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)

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)

Contrastively fine-tuned ESM-C 300M producing fixed-length protein embeddings where biological similarity maps to embedding proximity. Intended for retrieval, clustering, and nearest-neighbour transfer.

Deep learning-based multi-animal pose tracking and behavior classification, enabling automated quantification of social interactions and collective behavior across species (Nature Methods 2022, 2.2K+ stars)

Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.

Foundation model for tabular data that predicts on unseen real-world tables in a single forward pass, achieving accurate small-data classification and regression without task-specific training; widely applicable to scientific datasets with limited samples (7.4K+ stars, 2022-2026)

EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)

Technical Report 🧬

Library for fast calculations of **mo**lecula**r** **fe**at**u**re**s** from 3D structures for machine learning with a focus on steric descriptors.

High-accuracy PDF→Markdown/JSON/HTML conversion, specialized for tables/formulas/code blocks with benchmark scripts

OEO is a domain reference ontology for energy system modeling.

Parsers and algorithms for computational chemistry logfiles.

This 1,120,772,224-parameter nucleotide-level causal language model is a member of the eight-model MarinDNA v0.5 parameter-scaling ladder developed with Marin. This repository contains only the final step-215573 checkpoint from run dna-bolinas-scaling-v0.5-h1920-p1B-0dc6f4, with its tokenizer…

MarinDNA m5.1 is a 1.12B-parameter, nucleotide-level causal language model developed with Marin. This is the final m5.1 base-model checkpoint at step 59,158 from run dna-bolinas-mix-v0.9-p1B-i24-exp135-zoonomia-m5.1-bef41e, released with the A 1B standard Transformer rivals Evo 2 40B on variant…

linkset-automation is a set of tools to automatically generates CyTargetLinker linksets from different resources, starting with WikiPathways.

For a convenient overview and download list, visit our model page for this model.

Converts Protein Data Bank structures into 3D-printable models. Each polymer chain is meshed separately and written as a named object in a single 3MF file, so a multi-material printer can assign one filament per chain. Protein chains can be rendered as a solvent-excluded surface, a cartoon, or a backbone tube; nucleic acids as a tube-and-rung form with the strands of a duplex welded at every base pair. Press-fit magnet pockets are optionally placed at chain interfaces, so a complex comes apart where its subunits actually meet. All meshes are checked for watertightness before export.

PyTorch-based differentiable programming framework for physics-informed system identification, parametric constrained optimization, and model predictive control, integrating neural operators, neural ODEs, KANs, SINDy, and differentiable predictive control with 30+ tutorials (1.3k+ stars, BSD License)

Robust deep learning-based segmentation of >100 anatomical structures in CT and MR images, built on nnU-Net and widely adopted in clinical radiology and surgical planning workflows (2.6K+ stars)

Machine learning toolkit for many-body quantum systems, implementing neural quantum states, variational Monte Carlo, and tensor network algorithms to solve ground-state and dynamical problems in condensed matter physics and quantum chemistry (EPFL & collaborators, Nature Physics 2019/2022+, 670+ stars)

HealthGPT-LoRA is a biomedical question-answering model built by fine-tuning Meta Llama 3.2 3B Instruct using QLoRA (PEFT) on the PubMedQA dataset.

Python computational framework for analysis of single-molecule FRET data

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

Open-source LLM-powered R&D agent framework automating data-driven AI solution building through automated research, development, and evolution; achieves top open-source performance on MLE-Bench with dual Researcher-Developer agents and supports research copilot, data mining, Kaggle, and quant R&D workflows (13.6K+ stars, MIT License, 2025-2026)

Analysis of molecular dynamics trajectories.

ProtSent-V2 35M plus one more contrastive pass on a fresh draw of the corpus, with a DMS/ProteinGym CoSENT target and a Global Orthogonal Regularization term added.