AI Agent Skills¶
66 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 with MCP integration for any AI coding client (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, Antigravity, OpenCode, etc.).
General Purpose¶
Router skill for ToolUniverse tasks. First checks if specialized tooluniverse skills (54 skills covering disease/drug/target research, clinical decision support, genomics, transcriptomics, single-cell analysis, variant…
Research Skills¶
Detect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, ROR, IC), and biomedical evidence.
Comprehensive antibody engineering and optimization for therapeutic development. Covers humanization, affinity maturation, developability assessment, and immunogenicity prediction.
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibility.
Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs multi-database analysis covering clinical…
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment.
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions.
Search and retrieve clinical practice guidelines across 12+ authoritative sources including NICE, WHO, ADA, AHA/ACC, NCCN, SIGN, CPIC, CMA, CTFPHC, GIN, MAGICapp, PubMed, EuropePMC, TRIP, and OpenAlex.
Strategic clinical trial design feasibility assessment using ToolUniverse. Evaluates patient population sizing, biomarker prevalence, endpoint selection, comparator analysis, safety monitoring, and regulatory pathways.
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks clinical trials from ClinicalTrials.gov…
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets.
Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it with findings from 10 research dimensions.
Comprehensive drug-drug interaction (DDI) prediction and risk assessment. Analyzes interaction mechanisms (CYP450, transporters, pharmacodynamic), severity classification, clinical evidence grading, and provides…
Identify drug repurposing candidates using ToolUniverse for target-based, compound-based, and disease-driven strategies.
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections.
Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimensions (disambiguation, disease association, druggability, chemical matter, clinical precedent,…
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density),…
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports.
Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools.
Transform GWAS signals into actionable drug targets and repurposing opportunities. Performs locus-to-gene mapping, target druggability assessment, existing drug identification, safety profile evaluation, and clinical…
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions.
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 compare study designs, effect sizes, ancestry diversity, and…
Discover genes associated with diseases and traits using GWAS data from the GWAS Catalog (500,000+ associations) and Open Targets Genetics (L2G predictions).
Production-ready microscopy image analysis and quantitative imaging data skill for colony morphometry, cell counting, fluorescence quantification, and statistical analysis of imaging-derived measurements.
Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data. Analyze TCR/BCR repertoires to assess clonality, diversity, V(D)J gene usage, CDR3 characteristics, convergence, and predict…
Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and optional biomarkers (TMB, PD-L1, MSI status), performs systematic analysis…
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking.
Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction.
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem.
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments.
Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision medicine.
Comprehensive multi-omics disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers for systems-level understanding.
Construct and analyze compound-target-disease networks for drug repurposing, polypharmacology discovery, and systems pharmacology.
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk…
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles, interprets PRS percentiles, and assesses disease predisposition across conditions…
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials.
Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis…
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation.
Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and protein-protein interactions.
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data.
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering.
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.
Production-ready single-cell and expression matrix analysis using scanpy, anndata, and scipy. Performs scRNA-seq QC, normalization, PCA, UMAP, Leiden/Louvain clustering, differential expression (Wilcoxon, t-test,…
Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics…
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms.
Perform statistical modeling and regression analysis on biomedical datasets. Supports linear regression, logistic regression (binary/ordinal/multinomial), mixed-effects models, Cox proportional hazards survival…
Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inversions, translocations), assesses pathogenicity using ACMG-adapted criteria, evaluates gene…
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels).
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expression, variants, drug interactions, and literature.
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions.
Systematic clinical variant interpretation from raw variant calls to ACMG-classified recommendations with structural impact analysis.
Development Skills¶
Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology. Integrates tools from ToolUniverse’s 1,264+ tool library, creates missing tools when needed using devtu-create-tool,…
Automatically discover life science APIs online, create ToolUniverse tools, validate them, and prepare integration PRs.
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing.
TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs.
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions.
GitHub workflow for ToolUniverse - push code safely by moving temp files, activating pre-commit hooks, running tests, and cleaning staged files.
Optimize tool descriptions in ToolUniverse JSON configs for clarity and usability. Reviews descriptions for missing prerequisites, unexpanded abbreviations, unclear parameters, and missing usage guidance.
Optimize ToolUniverse skills for better report quality, evidence handling, and user experience. Apply patterns like tool verification, foundation data layers, disambiguation-first, evidence grading, quantified…
Detect and auto-install missing ToolUniverse research skills by checking common client skill directories and cloning from GitHub if absent.
Build AI scientist systems using ToolUniverse Python SDK for scientific research. Use when users need to access 1000++ scientific tools through Python code, create scientific workflows, perform drug discovery, protein…
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