AI Agent Skills¶
Specialized research workflows for ToolUniverse
ToolUniverse provides AI agent skills that teach agents how to conduct sophisticated scientific research. These skills combine multiple tools into expert-level workflows.
Important
Install all skills with one command:
npx skills add mims-harvard/ToolUniverse
Setup & Configuration¶
Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API wit…
General Purpose¶
Router skill for ToolUniverse tasks. First checks if specialized tooluniverse skills (105+ skills covering disease/drug/target research, gene-disea…
Research Skills¶
Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology. Integrates tools from ToolUniverse’s 1,264+ too…
Systematic ACMG/AMP variant classification using ToolUniverse tools. Given a genetic variant (HGVS, rsID, or gene+change), applies all 28 ACMG crit…
Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling of drug candidates using ADMETAI predictions, SwissADME d…
Detect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, ROR, IC), and biomedical evidenc…
> Map environmental/industrial chemicals to mechanistic adverse outcome pathways (AOPs) using AOPWiki, quantify toxicological hazard (PubChemTox GH…
Research aging biology, cellular senescence, and longevity using ToolUniverse. Covers senescence markers and pathways, age-related disease genetics…
Comprehensive antibody engineering and optimization for therapeutic development. Covers humanization, affinity maturation, developability assessmen…
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candid…
> Translate free-text tumor descriptions to OncoTree codes, look up cancer subtypes and tissue hierarchies, resolve UMLS/NCI cross-references, and …
> TCGA/GDC cancer genomics analysis – cohort construction, clinical metadata retrieval, somatic mutation profiling, copy number variation analysis…
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and opti…
Help researchers select and characterize cancer cell lines for experiments. Given a cancer type, gene of interest, or cell line name, profiles mole…
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Creates comprehensi…
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safet…
Find commercial sources for chemical compounds using ZINC, Enamine, eMolecules, and Mcule. Covers compound identification, vendor search, pricing, …
Comprehensive drug safety review integrating FDA labels, FAERS adverse event reports, disproportionality analysis, pharmacogenomics, clinical trial…
Search and retrieve clinical practice guidelines across 12+ authoritative sources including NICE, WHO, ADA, AHA/ACC, NCCN, SIGN, CPIC, CMA, CTFPHC,…
Strategic clinical trial design feasibility assessment using ToolUniverse. Evaluates patient population sizing, biomarker prevalence, endpoint sele…
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior trea…
Cross-species gene and sequence comparison, ortholog analysis, and evolutionary conservation assessment using ToolUniverse tools. Use when comparin…
Solve quantitative problems in biophysics, pharmacokinetics, epidemiology, toxicology, population genetics, and statistical mechanics. Provides rea…
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to iden…
> Add custom local tools to ToolUniverse and use them alongside the 1000+ built-in tools. Use this skill when a user wants to: create their own too…
Integrate statistical analysis results with biological knowledge from ToolUniverse tools. After computing associations or differential expression, …
Universal data access reference for scientific research. Teaches how to download bulk data, parse any scientific file format (VCF, h5ad, mzML, PDB,…
Find and evaluate research datasets for any scientific question. Teaches how to reason about data needs, search across public repositories, evaluat…
Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it…
Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), …
> Drug mechanism of action investigation – systematic strategy to trace a drug from its primary target through pathways to clinical outcomes, iden…
> Drug regulatory and approval research – FDA substance registry lookup, drug classification by ATC/EPC/MoA via RxClass, Orange Book generic avail…
Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies. Searches existing drugs fo…
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity,…
Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimensions (disambiguation, dise…
Ecology, biodiversity, and conservation biology research — species identification, invasive species assessment, pollinator ecology, population dyna…
Search and analyze cryo-EM maps, single particle structures, tomography datasets, and raw micrograph data from EMDB, EMPIAR, and CryoET Data Portal…
End-to-end epidemiological data analysis — from research question to statistical report. Covers study design assessment, dataset discovery and down…
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential m…
> Epigenomics and chromatin accessibility research – histone modification ChIP-seq data from ENCODE, CTCF binding and chromatin architecture, eQTL…
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structur…
Interpret results from CRISPR/shRNA genetic screens using DepMap essentiality data, constraint scores, pathway enrichment, protein networks, drugga…
Find and compare gene-disease associations across multiple databases (DisGeNET, OpenTargets, Monarch Initiative, OMIM, GenCC, Orphanet, ClinVar). P…
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supp…
> Research GPCR receptors, antibody structures, and protein interface analysis using GPCRdb, SAbDab, and PDBePISA. Retrieves receptor families, kno…
Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, …
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities…
Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar)….
Compare GWAS studies, perform meta-analyses, and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics to …
Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G pre…
Analyze HLA genes, MHC binding, epitope-MHC associations, and immunogenomics for transplant compatibility, vaccine design, and immunotherapy. Integ…
Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, …
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity…
Immunology research workflows using ToolUniverse tools. Covers antibody-antigen structural analysis (SAbDab, TheraSAbDab), immune protein interacti…
Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and opti…
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, p…
Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, bonding theory (covalency, orbital mix…
Detect and auto-install missing ToolUniverse research skills by checking common client skill directories and cloning from GitHub if absent. Use whe…
> KEGG-based disease-drug-variant research using KEGG Disease, Drug, Network, and Variant databases. Covers disease gene lookup, drug-target analys…
Analyze lipids, lipid metabolism, and lipid-disease associations using LIPID MAPS, HMDB, PubChem, KEGG, and CTD. Covers lipid identification, class…
Comprehensive literature deep research across any academic domain using 120+ ToolUniverse tools. Conducts subject disambiguation, systematic litera…
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (22…
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR da…
Metabolomics pathway analysis – metabolite identification, pathway mapping, disease associations, cross-database enrichment, and enzyme/gene linka…
Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keyword, retrieve taxonomic profile…
Analyze microbiome and metagenomics data using MGnify, GTDB, ENA, and literature tools. Search studies by biome/keyword, retrieve taxonomic profile…
Cross-species genetic analysis using model organism databases. Maps human genes to orthologs in mouse, fly, worm, zebrafish, yeast, and frog, then …
Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision …
Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-l…
Construct and analyze compound-target-disease networks for drug repurposing, polypharmacology discovery, and systems pharmacology. Builds multi-lay…
Neuroscience research and reasoning workflows using ToolUniverse tools. Covers computational neuroscience (rate models, integrate-and-fire neurons,…
Analyze non-coding RNAs (miRNAs, lncRNAs, circRNAs) using miRBase, LNCipedia, RNAcentral, Rfam, and target prediction databases. Covers ncRNA ident…
Teaches reasoning strategies for organic chemistry problems — reaction product prediction, spectroscopy interpretation, stereochemistry, and quanti…
Connect GWAS variants to biological pathways for drug target discovery. Maps disease-associated SNPs to causal genes via eQTL colocalization (GTEx)…
Guide pharmacogenomics (PGx) research – drug-gene interaction lookup, CPIC guideline retrieval, variant-drug annotation, allele function status, F…
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, …
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RC…
Research plant genes, pathways, and species using PlantReactome, Ensembl Plants, POWO, UniProt, KEGG, and literature tools. Covers plant pathway an…
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PR…
> Population genetics research using the 1000 Genomes Project (IGSR) – search populations by superpopulation ancestry (AFR, AMR, EAS, EUR, SAS), r…
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, geno…
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved th…
Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks …
Analyze post-translational modifications (PTMs) of proteins — modification sites, types, proteoforms, functional effects at PTM sites, and PTM-depe…
Predict and analyze protein 3D structure from amino acid sequence using ESMFold and AlphaFold. Covers de novo structure prediction (ESMFold for seq…
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural p…
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMP…
Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and p…
> Find and retrieve proteomics datasets from public repositories including MassIVE and ProteomeXchange (which aggregates PRIDE, PeptideAtlas, jPOST…
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identi…
> Rare disease genomics research – disease identification via Orphanet, causative gene discovery, gene-disease validity assessment via GenCC, path…
> Investigate transcription factor binding, cis-regulatory elements, chromatin accessibility, and regulatory variant annotation. Use when asked abo…
Regulatory variant interpretation – GWAS association lookup, eQTL analysis, chromatin state annotation, regulatory element overlap, and trait onto…
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC s…
Build AI scientist systems using ToolUniverse Python SDK for scientific research. Use when users need to access 1000++ scientific tools through Pyt…
Retrieve and analyze biological sequences – gene/protein sequences from NCBI, Ensembl, and UniProt. Search nucleotide databases, fetch by accessio…
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence …
“Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Lei…
> Find, characterize, and source small molecules for chemical biology and drug discovery. Covers compound identification (PubChem, ChEMBL), structu…
Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissu…
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-b…
Perform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regression (binary/ordinal/multin…
Research stem cells, iPSCs, organoids, and cell differentiation using ToolUniverse tools. Covers pluripotency marker identification, differentiatio…
Integrate structural biology data with proteomics for drug target validation. Retrieves protein structures from PDB (RCSB, PDBe), AlphaFold predict…
Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inversions, translocations), a…
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Per…
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expres…
> Assess chemical and drug toxicity via adverse outcome pathways, real-world adverse event signals, and toxicogenomic evidence. Integrates AOPWiki …
Design and evaluate vaccine candidates using computational immunology tools. Covers epitope prediction (MHC-I/II binding via IEDB), population cove…
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions…
> Comprehensive functional annotation of protein variants — pathogenicity, population frequency, structural context, and clinical significance. Int…
Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis. Aggregates ev…
> End-to-end variant-to-mechanism analysis: given a genetic variant (rsID or coordinates), trace its functional impact from regulatory context (GWA…
Development Skills¶
Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs. Performs gap analysis to id…
> Code quality patterns and guidelines for ToolUniverse tool development. Apply when writing, fixing, or refactoring tool Python code in the ToolUn…
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniv…
TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code, …
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUni…
GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files. Us…
Optimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbre…
Optimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation d…
> Orchestrate the full ToolUniverse self-improvement cycle: discover APIs, create tools, test with researcher personas, fix issues, optimize skills…
How to Use Skills¶
After installation, skills are available in your AI coding agent. Some agents activate skills automatically based on your questions, while others may require you to explicitly mention the skill name.
Ask: “Research aspirin comprehensively”
Activates: tooluniverse-drug-research
Ask: “Analyze EGFR as a drug target”
Activates: tooluniverse-target-research
Ask: “Generate disease report for diabetes”
Activates: tooluniverse-disease-research
Ask: “Deep literature review on CRISPR”
Activates: tooluniverse-literature-deep-research