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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.

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

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)

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 Intended as a successor to Mycobrowser, which is no longer maintained.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)

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

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_.

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)

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)

Deep learning library for Chemistry based on Tensorflow

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.

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.

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.

ECMWF's unified framework and command-line tool to run AI-based weather forecasting models (GraphCast, Aurora, Pangu, NeuralGCM, FourCastNet) with operational ECMWF data infrastructure, enabling standardized inference and benchmarking across state-of-the-art meteorological AI systems (ECMWF, 576+ stars)

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.

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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)

Fast, differentiable, JIT-free finite element library for PyTorch enabling GPU-native PDE solving with native autograd, tensorized assembly, and sparse linear algebra; part of the TensorGalerkin framework (218+ stars, Apache 2.0)