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
1---2name: tooluniverse3description: Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more4---56# ToolUniverse78Gateway 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.910## Overview1112ToolUniverse 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.1314## Usage1516### Run any ToolUniverse tool:17```bash18python3 {baseDir}/scripts/tooluniverse_run.py --tool UniProt_get_entry_by_accession \19 --args '{"accession": "P05067"}'20```2122### Discover available tools:23```bash24python3 {baseDir}/scripts/tooluniverse_list.py25python3 {baseDir}/scripts/tooluniverse_list.py --search "compound"26python3 {baseDir}/scripts/tooluniverse_list.py --search "protein" --format json27python3 {baseDir}/scripts/tooluniverse_list.py --info PubChem_get_compound_properties_by_CID28```2930## Parameters (tooluniverse_run.py)3132| Parameter | Description | Default |33|-----------|-------------|---------|34| `--tool` | ToolUniverse tool name (exact, case-sensitive) | Required |35| `--args` | Tool arguments as a JSON string | `{}` |36| `--format` | Output format: json, summary | json |37| `--no-cache` | Disable result caching | false |3839## Available Research Workflows (54+)4041### Drug Discovery42- binder-discovery, drug-repurposing, drug-target-validation, drug-drug-interaction43- chemical-safety, network-pharmacology, pharmacovigilance, adverse-event-detection4445### Genomics & Variants46- gwas-trait-to-gene, gwas-snp-interpretation, gwas-fine-mapping, gwas-study-explorer47- variant-analysis, variant-interpretation, structural-variant-analysis48- crispr-screen-analysis, cancer-variant-interpretation4950### Omics & Transcriptomics51- rnaseq-deseq2, single-cell, epigenomics, spatial-transcriptomics52- proteomics-analysis, metabolomics, metabolomics-analysis53- multi-omics-integration, gene-enrichment, expression-data-retrieval5455### Disease & Clinical56- disease-research, rare-disease-diagnosis, clinical-trial-matching57- clinical-trial-design, clinical-guidelines, precision-oncology58- precision-medicine-stratification, immunotherapy-response-prediction, infectious-disease5960### Proteins & Sequences61- sequence-retrieval, protein-structure-retrieval, protein-interactions62- protein-therapeutic-design, antibody-engineering, phylogenetics6364### Systems Biology65- systems-biology, immune-repertoire-analysis, polygenic-risk-score66- gwas-drug-discovery, multiomic-disease-characterization, statistical-modeling6768### Data Retrieval69- chemical-compound-retrieval, target-research, literature-deep-research7071## Examples7273```bash74# Retrieve protein entry75python3 {baseDir}/scripts/tooluniverse_run.py \76 --tool UniProt_get_entry_by_accession --args '{"accession": "P05067"}'7778# Get compound properties79python3 {baseDir}/scripts/tooluniverse_run.py \80 --tool PubChem_get_compound_properties_by_CID --args '{"cid": 1983}'8182# Search PubMed83python3 {baseDir}/scripts/tooluniverse_run.py \84 --tool PubMed_search_articles --args '{"query": "Alzheimer amyloid", "max_results": 10}'8586# List tools related to GWAS87python3 {baseDir}/scripts/tooluniverse_list.py --search "gwas"88```8990## Installation9192```bash93pip install tooluniverse94```9596## Notes9798- Tool names are exact and case-sensitive — use `tooluniverse_list.py` to discover99- Results are cached by default; use `--no-cache` for fresh data100- All outputs are JSON for downstream tool chaining101- Set API keys via environment variables as required by individual tools
lamm-mit