LabClaw – Skill Operating Layer for Stanford LabOS & Next-Gen AI Co-Scientists

Powering dry-lab reasoning, protocol composition, and agentic workflows to close the loop with LabOS XR/wet-lab execution.

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LabClaw is a skill library, not a monolithic software package. You can install the full collection or copy only the skill folders that match your research workflows.

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Overview

LabClaw packages 211 production-ready SKILL.md files for biomedical AI workflows across biology, lab automation, vision/XR, drug discovery, medicine, data science, and literature research. Each skill teaches an OpenClaw-compatible agent when to use a tool, how to call it, and what kind of output to produce.

The collection is designed for researchers who want a practical, modular skill layer instead of a generic prompt bundle. You can use it as a broad starter library, or cherry-pick only the subfolders relevant to your lab, team, or project.

At a Glance

Domain	Skills	Focus
🧬 Biology & Life Sciences	66	Bioinformatics, single-cell, genomics, proteomics, multi-omics, databases
🤖 LabOS & Automation	7	Lab robots, LIMS/ELN, cloud platforms, protocol management
👁️ Vision & XR	5	Hand tracking, 3D pose estimation, segmentation, egocentric vision
💊 Pharmacy & Drug Discovery	36	Cheminformatics, molecular ML, docking, target research, pharmacology, drug databases
🏥 Medical & Clinical	20	Clinical trials, precision medicine, oncology, infectious disease, medical imaging
⚙️ General & Data Science	48	Statistics, machine learning, data management, visualization, scientific writing
📚 Literature & Search	29	Academic search, biomedical databases, multi-source discovery, patents, grants, citations

Representative Workflows

Workflow	Example skills
Single-cell and spatial omics	anndata, scanpy, tooluniverse-spatial-transcriptomics
Drug discovery and molecular design	rdkit, diffdock, tooluniverse-drug-repurposing
Clinical and precision medicine	clinical, tooluniverse-precision-oncology, clinicaltrials-database
Statistics, ML, and figure generation	statistics, scikit-learn, scientific-visualization
Literature review and reporting	pubmed-search, citation-management, scientific-writing

3-Second Quick Start

Just send the message to OpenClaw:

install https://github.com/wu-yc/LabClaw

Use Cases

In Lab (with XR):

Repository Layout

LabClaw/
├── README.md
├── README.zh-CN.md
└── skills/
    ├── bio/         # 66 skills: genomics, proteomics, single-cell, systems biology
    ├── labos/       # 7 skills: lab robots, LIMS/ELN, cloud platforms, protocols
    ├── vision/      # 5 skills: hand tracking, 3D pose, segmentation, egocentric
    ├── pharma/      # 36 skills: cheminformatics, docking, target discovery, pharmacology
    ├── med/         # 20 skills: clinical research, precision medicine, oncology, imaging
    ├── general/     # 48 skills: statistics, ML, visualization, writing, reproducibility
    └── literature/  # 29 skills: search, databases, grants, patents, citations

Related Repositories

These projects are especially relevant if you want to place LabClaw in the broader biomedical-agent ecosystem:

Repository	Why it matters
openclaw/openclaw	The main runtime that loads workspace skills and provides the skills platform, onboarding flow, and agent workspace model that LabClaw is designed to fit into.
mims-harvard/ToolUniverse	A large AI-scientist tool ecosystem. LabClaw includes many tooluniverse-* skills across omics, drug discovery, clinical workflows, and literature research.
snap-stanford/Biomni	A complementary biomedical AI agent project. LabClaw already includes a biomni skill, making Biomni a natural reference point for users exploring autonomous biomedical research agents.

Full Skill Catalog

The original catalog is preserved below, but grouped into collapsible sections to make browsing easier on GitHub.

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🧬 Biology & Life Sciences — 66 skills

Tools for genomics, transcriptomics, proteomics, single-cell analysis, structural biology, systems biology, and lab automation.

66 skills  ·  skills/bio/

Bioinformatics Core

Skill	Description
arboreto	Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when ...
bioinformatics	Computational biology and genomics analysis pipelines. GENERAL: not locked to any specific tool — use Scanpy, Seurat, DE...
biomni	Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular...
biopython	Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics,...
cobrapy	Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology a...
etetoolkit	Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI ...
geniml	This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for traini...
gget	Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold str...
gtars	High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regio...
hypogenic	Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore ...
scikit-bio	Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ord...

Single-cell & Spatial Transcriptomics

Skill	Description
anndata	Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the...
cellxgene-census	Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or...
scanpy	Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), cl...
scvi-tools	Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning...
tooluniverse-single-cell	Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, nor...
tooluniverse-spatial-omics-analysis	Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatia...
tooluniverse-spatial-transcriptomics	Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFIS...
umap-learn	UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.

Genomics, NGS & Variant Analysis

Skill	Description
deeptools	NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for...
pydeseq2	Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR corre...
pysam	Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calc...
tooluniverse-crispr-screen-analysis	Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activa...
tooluniverse-epigenomics	Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (Cp...
tooluniverse-expression-data-retrieval	Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
tooluniverse-gene-enrichment	Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 4...
tooluniverse-gwas-drug-discovery	Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, targe...
tooluniverse-gwas-finemapping	Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Compu...
tooluniverse-gwas-snp-interpretation	Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open ...
tooluniverse-gwas-study-explorer	Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog an...
tooluniverse-gwas-trait-to-gene	Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Ope...
tooluniverse-immune-repertoire-analysis	Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to ...
tooluniverse-polygenic-risk-score	Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic r...
tooluniverse-rnaseq-deseq2	Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion esti...
tooluniverse-sequence-retrieval	Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, ...
tooluniverse-structural-variant-analysis	Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inv...
tooluniverse-variant-analysis	Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation f...
tooluniverse-variant-interpretation	Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural imp...

Proteomics & Structural Biology

Skill	Description
alphafold-database	Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, ana...
esm	Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, ...
pyopenms	Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, pr...
tooluniverse-protein-interactions	Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retr...
tooluniverse-protein-structure-retrieval	Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and...
tooluniverse-proteomics-analysis	Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational ...
uniprot-database	Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflow...

Multi-Omics & Systems Biology

Skill	Description
matchms	Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity s...
tooluniverse-metabolomics	Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics dat...
tooluniverse-metabolomics-analysis	Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Pro...
tooluniverse-multi-omics-integration	Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for sys...
tooluniverse-multiomic-disease-characterization	Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and thera...
tooluniverse-phylogenetics	Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary met...
tooluniverse-systems-biology	Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathw...

Biological Databases

Skill	Description
brenda-database	Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, a...
clinpgx-database	Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele func...
cosmic-database	Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions...
ena-database	Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by acce...
ensembl-database	Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative...
kegg-database	Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug int...
metabolomics-workbench-database	Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/...
reactome-database	Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions...
string-database	Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment...

Lab Platforms & Imaging

Skill	Description
flowio	Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to C...
histolab	Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, sta...
lamindb	This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable...
omero-integration	Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotation...
pathml	Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (C...

🤖 LabOS & Laboratory Automation — 7 skills

Tools for lab robotics, LIMS/ELN systems, cloud platforms, and scientific protocol management. Optimized for Stanford LabOS workflows and automated laboratory research.

7 skills  ·  skills/labos/

Lab Robotics & Automation

Skill	Description
pylabrobot	Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors. Best for complex workflows, multi-vendor setups, simulation.
opentrons-integration	Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility.

LIMS/ELN Systems

Skill	Description
benchling-integration	Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
labarchive-integration	Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with laboratory workflows, for ELN automation.

Lab Cloud Platforms

Skill	Description
latchbio-integration	Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless bioinformatics apps, for cloud bioinformatics.
dnanexus-integration	DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/CRAM processing, for cloud genomic analysis.

Protocol Management

Skill	Description
protocolsio-integration	Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protoco...

👁️ Vision & XR — 5 skills

Tools for hand tracking, 3D pose estimation, hand-object segmentation, and egocentric vision. Optimized for XR/AR applications, smart glasses interfaces, and computer vision research.

5 skills  ·  skills/vision/

Hand Detection & Tracking

Skill	Description
handtracking	Real-time hand detection in egocentric videos using victordibia/handtracking. Outputs bounding boxes for hands, specifically trained on EgoHands dataset. Lightweight and fast for egocentric view applications.
hands-3d-pose	High-quality 3D hand pose estimation for egocentric videos (ECCV 2024). Provides 3D joint keypoints and skeleton visualization projected to 2D. Optimized for daily egocentric activities with state-of-the-art accuracy.

Segmentation & Analysis

Skill	Description
egohos-segmentation	Egocentric hand-object segmentation (EgoHOS) - pixel-level hand and object masks in egocentric videos. Specialized for hand-object interaction scenarios with pixel-accurate masks for detailed interaction analysis.

Multi-View 3D Tracking

Skill	Description
hot3d	HOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art multi-view 3D hand pose, object pose, and hand-object interaction tracking with millimeter accuracy.
hand-tracking-toolkit	Facebook Research hand tracking evaluation and visualization toolkit. Supports loading HOT3D data, computing metrics (PA-MPJPE, AUC), visualizing 3D pose projections, and generating tracking evaluation reports.

💊 Pharmacy & Drug Discovery — 36 skills

Tools for cheminformatics, molecular docking, drug design, pharmacology, pharmacovigilance, and drug databases.

36 skills  ·  skills/pharma/

Cheminformatics & Molecular Design

Skill	Description
chemistry	Computational chemistry, cheminformatics, and drug discovery workflows.
datamol	Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery inc...
deepchem	Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditi...
medchem	Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity m...
molfeat	Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMIL...
rdkit	Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprin...
rowan	Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa pr...

Molecular Machine Learning

Skill	Description
pytdc	Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecula...
torch_geometric	Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, mole...
torchdrug	PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug dis...

Molecular Docking & Protein Therapeutics

Skill	Description
adaptyv	Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experime...
diffdock	Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual scre...
tooluniverse-antibody-engineering	Comprehensive antibody engineering and optimization for therapeutic development. Covers humanization, affinity maturatio...
tooluniverse-binder-discovery	Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates act...
tooluniverse-protein-therapeutic-design	Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for bac...

Drug Research & Target Discovery

Skill	Description
tooluniverse-drug-repurposing	Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies....
tooluniverse-drug-research	Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness...
tooluniverse-drug-target-validation	Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimen...
tooluniverse-target-research	Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, int...

Pharmacology & Safety

Skill	Description
tooluniverse-adverse-event-detection	Detect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, ROR, ...
tooluniverse-chemical-safety	Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label ...
tooluniverse-drug-drug-interaction	Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, trans...
tooluniverse-network-pharmacology	Construct and analyze compound-target-disease networks for drug repurposing, polypharmacology discovery, and systems pha...
tooluniverse-pharmacovigilance	Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disprop...

Chemical & Drug Databases

Skill	Description
chembl-database	Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity...
chembl-search	Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu seman...
drug-discovery-search	End-to-end drug discovery platform combining ChEMBL compounds, DrugBank, targets, and FDA labels. Natural language power...
drug-labels-search	Search FDA drug labels with natural language queries. Official drug information, indications, and safety data via Valyu.
drugbank-database	Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, ta...
drugbank-search	Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety dat...
fda-database	Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identificat...
open-targets-search	Search Open Targets drug-disease associations with natural language queries. Target validation powered by Valyu semantic...
opentargets-database	Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/o...
pubchem-database	Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/s...
tooluniverse-chemical-compound-retrieval	Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality asse...
zinc-database	Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for dockin...

🏥 Medical & Clinical — 20 skills

Tools for clinical research, precision medicine, oncology, infectious disease, and medical imaging.

20 skills  ·  skills/med/

Clinical Research & Trials

Skill	Description
clinical	Clinical study design, statistical analysis, and regulatory compliance for medical research.
clinical-decision-support	Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, inclu...
clinical-reports	Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/l...
tooluniverse-clinical-guidelines	Search and retrieve clinical practice guidelines across 12+ authoritative sources including NICE, WHO, ADA, AHA/ACC, NCC...
tooluniverse-clinical-trial-design	Strategic clinical trial design feasibility assessment using ToolUniverse. Evaluates patient population sizing, biomarke...
tooluniverse-clinical-trial-matching	AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alt...
treatment-plans	Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports ...

Precision Medicine & Oncology

Skill	Description
tooluniverse-cancer-variant-interpretation	Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR ...
tooluniverse-disease-research	Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file a...
tooluniverse-immunotherapy-response-prediction	Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, ...
tooluniverse-infectious-disease	Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxo...
tooluniverse-precision-medicine-stratification	Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Give...
tooluniverse-precision-oncology	Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations,...
tooluniverse-rare-disease-diagnosis	Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches sy...

Medical Imaging, Devices & Regulatory

Skill	Description
iso-13485-certification	Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems....
neurokit2	Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and ...
neuropixels-analysis	Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sort...
pydicom	Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when readin...
pyhealth	Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. T...
tooluniverse-image-analysis	Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fl...

⚙️ General & Data Science — 48 skills

General-purpose tools for statistics, machine learning, data management, visualization, and scientific writing.

48 skills  ·  skills/general/

Statistics & Mathematical Modeling

Skill	Description
matlab	MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when the user needs help with MATLAB syntax, functions, or wants to convert between MATLAB and Python code. Scripts can be executed with MATLAB or the open-source GNU Octave interpreter.
pymc	Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posteri...
pymoo	Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, ...
scikit-survival	Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill w...
statistical-analysis	Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for you...
statistics	Comprehensive statistical methodology for scientific research. Covers test selection, assumption verification, power ana...
statsmodels	Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with det...
sympy	Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation task...
tooluniverse-statistical-modeling	Perform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regres...

Machine Learning & AI

Skill	Description
aeon	This skill should be used for time series machine learning tasks including classification, regression, clustering, forec...
pytorch-lightning	Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-G...
scikit-learn	Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), un...
shap	Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining mac...
transformers	This skill should be used when working with pre-trained transformer models for natural language processing, computer vis...

Data Management & Computing

Skill	Description
dask	Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code ...
exploratory-data-analysis	Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be ...
fair-data	Guidelines for making scientific data FAIR: Findable, Accessible, Interoperable, and Reusable.
geopandas	Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when wor...
get-available-resources	This skill should be used at the start of any computationally intensive scientific task to detect and report available s...
markitdown	Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcrip...
networkx	Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working w...
polars	Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory...
reproducibility-checklist	Ensure research is reproducible, transparent, and meets open science standards.
vaex	Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex ex...
zarr-python	Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible,...

Visualization

Skill	Description
matplotlib	Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creat...
plotly	Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboard...
scientific-diagram-generation	AI-powered scientific illustration generation using Gemini Image models. Creates publication-quality mechanism diagrams,...
scientific-visualization	Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, si...
seaborn	Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and catego...
visualization	Publication-quality scientific figure generation. GENERAL: language-agnostic (R, Python, Julia, or any tool).

Scientific Writing & Presentation

Skill	Description
article-writing	Write articles, guides, blog posts, tutorials, newsletter issues, and other long-form content in a distinctive voice der...
hypothesis-generation	Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to for...
latex-posters	Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presen...
peer-review	Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific c...
pptx-generation	Create publication-quality academic presentations (.pptx) for group meetings, thesis defenses, conference talks, and pos...
pptx-posters	Create research posters using HTML/CSS that can be exported to PDF or PPTX. Use this skill ONLY when the user explicitly...
protocol-writing	Write clear, reproducible experimental protocols and Standard Operating Procedures (SOPs) for any scientific discipline.
scholar-evaluation	Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research ...
science-communication	Translate complex scientific findings into engaging content for non-specialist audiences.
scientific-brainstorming	Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary conne...
scientific-critical-thinking	Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and ...
scientific-slides	Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations,...
scientific-writing	Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points)...
venue-templates	Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publicatio...
writing	Scientific manuscript writing across all formats, fields, and journals.

IP, Regulatory & Reporting

Skill	Description
patent-drafting	Draft patent applications for scientific inventions, covering claims, specification, and prior art analysis.
regulatory-submission	Prepare regulatory submissions for drugs, biologics, devices, and diagnostics.

📚 Literature & Search — 29 skills

Tools for academic search, database queries, citation management, and literature review.

29 skills  ·  skills/literature/

Biomedical Literature Search

Skill	Description
academic-literature-search	Use this skill when the user asks to search for academic papers, retrieve literature, generate citations, format referen...
biomedical-search	Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Val...
biorxiv-database	Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by...
biorxiv-search	Search bioRxiv biology preprints with natural language queries. Semantic search powered by Valyu.
literature	Comprehensive academic literature search and synthesis across 15+ sources.
literature-review	Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic...
literature-search	Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by V...
medrxiv-search	Search medRxiv medical preprints with natural language queries. Powered by Valyu semantic search.
pubmed-database	Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management....
pubmed-search	Search PubMed biomedical literature with natural language queries powered by Valyu semantic search. Full-text access, in...
tooluniverse-literature-deep-research	Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction....

Genomic & Clinical Databases

Skill	Description
clinical-trials-search	Search ClinicalTrials.gov with natural language queries. Find clinical trials, enrollment, and outcomes using Valyu sema...
clinicaltrials-database	Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial detail...
clinvar-database	Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, ...
gene-database	Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotype...
geo-database	Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retr...
gwas-database	Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-value...
hmdb-database	Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomark...
openalex-database	Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academi...
pdb-database	Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmC...

Multi-Source Search & Discovery

Skill	Description
arxiv-search	Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic sea...
bioservices	Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Re...
perplexity-search	Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skil...
research-lookup	Look up current research information using Perplexity Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter....

Patents, Grants & Citation Management

Skill	Description
citation-management	Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate m...
patents-search	Search global patents with natural language queries. Prior art, patent landscapes, and innovation tracking via Valyu.
research-grants	Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review crite...
review-writing	Use this skill when the user asks to write a literature review, review article, or 综述 based on an outline. Trigger keywo...
uspto-database	Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSD...

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Skill Format

Every SKILL.md follows a consistent structure:

# Skill Name
## Overview        — what this skill enables
## When to Use     — trigger conditions for the AI agent
## Key Capabilities — specific tools, APIs, parameters
## Usage Examples  — concrete code or workflow examples

Credits

Skills curated by Yingcheng (Charles) Wu, Jinglin Jian, Zhe Zhao at Le Cong Lab of Stanford & Mengdi Wang Lab at Princeton.

License

MIT License

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