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 with MCP integration for any AI coding client (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Tra…
General Purpose¶
General strategies for using ToolUniverse effectively with 10000+ scientific tools. Covers tool discovery, multi-hop queries, comprehensive researc…
Research Skills¶
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candid…
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Creates comprehensi…
Generate comprehensive disease research reports using 100+ ToolUniverse tools. Creates a detailed markdown report file and progressively updates it…
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,…
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structur…
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, p…
Conduct comprehensive literature research with target disambiguation, evidence grading, and structured theme extraction. Creates a detailed report …
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, …
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved th…
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…
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identi…
Build AI scientist systems using ToolUniverse Python SDK for scientific research. Use when users need to access 1000++ scientific tools through Pyt…
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence …
Gather comprehensive biological target intelligence from 9 parallel research paths covering protein info, structure, interactions, pathways, expres…
Development Skills¶
Create new scientific tools for ToolUniverse framework with proper structure, validation, and testing. Use when users need to add tools to ToolUniv…
Comprehensive documentation quality system for ToolUniverse combining automated validation with modern Sphinx-Design patterns. Manages interactive …
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUni…
Fix failing ToolUniverse tools by diagnosing test failures, identifying root causes, implementing fixes, and validating solutions. Use when ToolUni…
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…
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