mims-harvard

mims-harvard/ToolUniverse

Plugin Claude Code

Plugin marketplace listing 1 plugin: tooluniverse.

mims-harvard/ToolUniverse

Plugin Claude Code

1000+ scientific research tools for biology, chemistry, medicine, and data science. Access PubMed, UniProt, PubChem, TCGA, NHANES, GWAS Catalog, and hundreds more databases through a unified MCP interface. Includes 120+ specialized research skills for genomics, drug discovery, clinical analysis, protein variant…

mims-harvard/ToolUniverse

MCP server Claude CodeCodexCursor +2

A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows. Runs locally from the tooluniverse Python package. Needs 3 environment variables to run.

mims-harvard/ToolUniverse

Agent

Autonomous scientific research agent with access to 1000+ databases. Use for complex research questions that require searching multiple databases, analyzing data, and synthesizing findings.

mims-harvard/ToolUniverse

Command

Side-by-side comparison of N items (drugs, targets, diseases, variants, trials, etc.) with a domain-appropriate column set, structured tabular output, and per-cell source citation. Use when the user wants to evaluate alternatives, not when they want a profile of a single item. Enforces the comparison structure that…

mims-harvard/ToolUniverse

Command

Take a specific scientific claim and confirm or refute it across 3+ independent databases, then report concordance. Use before publishing, citing, or acting on a fact when you want to know how strongly it's supported. Forces multi-source verification that the agent doesn't naturally enforce.

mims-harvard/ToolUniverse

Command

Run a graded mini-review on a topic across many literature sources, adaptively chosen by domain — a core multi-field set (PubMed, EuropePMC, OpenAlex, Semantic Scholar) plus domain-specific indexes (ArXiv/DBLP for CS, InspireHEP for physics, PubTator/PMC/clinical guidelines for biomedical, Crossref/CORE/DOAJ/Fatcat…

mims-harvard/ToolUniverse

Command

Conduct a multi-database scientific research investigation inline in the current chat. Same operating discipline as the /tooluniverse:researcher agent (look up specific claims, cross-validate, honest INDETERMINATE) — but runs in this conversation so you can watch each step, follow up, and refine, instead of receiving…

mims-harvard/ToolUniverse

Command

Review current or supplied work against the user's actual goal, report evidence-backed strengths, gaps, risks, and fixes, and give a plain-language completion verdict. Qualitative by default; only score or grade when explicitly requested.

mims-harvard/ToolUniverse

Command

Set up ToolUniverse API keys. Opens a graphical setup page (or guides you in chat) listing every key tools can use, with registration links, and saves them permanently to a .env that the MCP server, CLI, and SDK all read. Use when a tool reports a missing API key or when first configuring ToolUniverse.

mims-harvard/ToolUniverse

Command

Resolve an identifier across all relevant namespaces (HGNC symbol, Ensembl, UniProt, NCBI Gene ID, RefSeq, MGI, OMIM, ChEMBL, PubChem, etc.). Detects the input namespace automatically, picks the right resolver tool, and returns a complete cross-reference table. Use when you have an ID in one namespace and need it in…

mims-harvard/ToolUniverse

Command

Check whether cited references are real and accurately described — confirms each citation actually exists and that its title/authors/year/journal/DOI match what's claimed, using independent databases (Crossref, DataCite, PubMed, OpenAlex, Semantic Scholar, EuropePMC, plus domain-specific sources like…

mims-harvard/ToolUniverse

Hook

Runs when a session starts, executing astral.sh (2 commands). From mims-harvard/ToolUniverse.

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Install and configure ToolUniverse for any use case — MCP server (chat-based), CLI (command line with 9 subcommands), or Python SDK (Coding API with 3 calling patterns). Covers uv/uvx setup, MCP configuration for 12+ AI clients (Cursor, Claude Desktop, Windsurf, VS Code, Codex, Gemini CLI, Trae, Cline, etc.), full CLI…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Systematic ACMG/AMP germline variant classification with all 28 criteria (PVS1, PS1-4, PM1-6, PP1-5, BA1, BS1-4, BP1-7) for clinical significance. Produces 5-tier verdict (Pathogenic / Likely Pathogenic / VUS / Likely Benign / Benign) with cited evidence per criterion. Use for variant interpretation, VUS resolution…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Comprehensive ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) profiling for drug candidates. Integrates ADMET-AI predictions, SwissADME drug-likeness, PubChemTox experimental toxicity, ChEMBL clinical data, Lipinski rule-of-five, and CYP interaction data. Use for drug-likeness assessment, BBB…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Detect and analyze adverse drug event signals using FDA FAERS reports, drug labels, and disproportionality statistics (PRR, ROR, IC). Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, regulatory submissions, and…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Map environmental and industrial chemicals to adverse outcome pathways (AOPs) — molecular initiating event to organ-level toxicity. Uses AOPWiki, GHS classification, IARC carcinogen status, and LD50 data. Use for environmental/industrial chemical risk assessment, regulatory-grade hazard characterization, and AOP…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Aging biology, cellular senescence, and longevity research. Covers senescence markers (p16/CDKN2A, SASP, SA-beta-gal), aging hallmarks, senolytic drug discovery (dasatinib+quercetin, fisetin, navitoclax), epigenetic clocks, telomere biology, and longevity GWAS. Use for senescence-pathway analysis, age-related disease…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Therapeutic antibody engineering and optimization, lead-to-clinical-candidate. Covers sequence humanization (germline alignment, framework retention), affinity maturation, developability (aggregation, stability, PTMs), structure modeling (AlphaFold/PDB CDR analysis), immunogenicity prediction, and manufacturing…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Install, set up, verify, update, pin, uninstall, or troubleshoot the ToolUniverse plugin on Google Antigravity (AGY / Antigravity IDE / Antigravity 2.0). ALWAYS consult this skill for any of those — don't answer from memory, because the exact CLI name (agy), the "agy plugin install " flow, the uvx tooluniverse MCP…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Answer biomedical FACTUAL / recall / multiple-choice questions by querying ToolUniverse database tools instead of answering from memory. Triggers on any 'which gene/drug/variant/disease/pathway/miRNA/TF...' lookup, any question phrased 'according to ' (DisGeNet, OMIM, MSigDB, miRDB, GTRD, MGI, Ensembl, ClinVar…

mims-harvard/ToolUniverse

Skill Claude CodeCodex

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent…