lamm-mit/tooluniverse

ToolUniverse

Gateway to 1000+ machine learning models, databases, APIs, and scientific packages via Harvard's ToolUniverse ecosystem. Covers drug discovery, genomics, proteomics, clinical research, metabolomics, multi-omics, and more.

Overview

ToolUniverse standardizes access to scientific tools through a unified tu.run() interface. This skill wraps that interface so agents can call any ToolUniverse tool and receive JSON output compatible with the scienceclaw artifact system.

Usage

Run any ToolUniverse tool:

python3 {baseDir}/scripts/tooluniverse_run.py --tool UniProt_get_entry_by_accession \
    --args '{"accession": "P05067"}'

Discover available tools:

python3 {baseDir}/scripts/tooluniverse_list.py
python3 {baseDir}/scripts/tooluniverse_list.py --search "compound"
python3 {baseDir}/scripts/tooluniverse_list.py --search "protein" --format json
python3 {baseDir}/scripts/tooluniverse_list.py --info PubChem_get_compound_properties_by_CID

Parameters (tooluniverse_run.py)

| Parameter | Description | Default | |-----------|-------------|---------| | --tool | ToolUniverse tool name (exact, case-sensitive) | Required | | --args | Tool arguments as a JSON string | {} | | --format | Output format: json, summary | json | | --no-cache | Disable result caching | false |

Available Research Workflows (54+)

Drug Discovery

• binder-discovery, drug-repurposing, drug-target-validation, drug-drug-interaction
• chemical-safety, network-pharmacology, pharmacovigilance, adverse-event-detection

Genomics & Variants

• gwas-trait-to-gene, gwas-snp-interpretation, gwas-fine-mapping, gwas-study-explorer
• variant-analysis, variant-interpretation, structural-variant-analysis
• crispr-screen-analysis, cancer-variant-interpretation

Omics & Transcriptomics

• rnaseq-deseq2, single-cell, epigenomics, spatial-transcriptomics
• proteomics-analysis, metabolomics, metabolomics-analysis
• multi-omics-integration, gene-enrichment, expression-data-retrieval

Disease & Clinical

• disease-research, rare-disease-diagnosis, clinical-trial-matching
• clinical-trial-design, clinical-guidelines, precision-oncology
• precision-medicine-stratification, immunotherapy-response-prediction, infectious-disease

Proteins & Sequences

• sequence-retrieval, protein-structure-retrieval, protein-interactions
• protein-therapeutic-design, antibody-engineering, phylogenetics

Systems Biology

• systems-biology, immune-repertoire-analysis, polygenic-risk-score
• gwas-drug-discovery, multiomic-disease-characterization, statistical-modeling

Data Retrieval

• chemical-compound-retrieval, target-research, literature-deep-research

Examples

# Retrieve protein entry
python3 {baseDir}/scripts/tooluniverse_run.py \
    --tool UniProt_get_entry_by_accession --args '{"accession": "P05067"}'

# Get compound properties
python3 {baseDir}/scripts/tooluniverse_run.py \
    --tool PubChem_get_compound_properties_by_CID --args '{"cid": 1983}'

# Search PubMed
python3 {baseDir}/scripts/tooluniverse_run.py \
    --tool PubMed_search_articles --args '{"query": "Alzheimer amyloid", "max_results": 10}'

# List tools related to GWAS
python3 {baseDir}/scripts/tooluniverse_list.py --search "gwas"

Installation

pip install tooluniverse

Notes

• Tool names are exact and case-sensitive — use tooluniverse_list.py to discover
• Results are cached by default; use --no-cache for fresh data
• All outputs are JSON for downstream tool chaining
• Set API keys via environment variables as required by individual tools