Agent skill

Tooluniverse

Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more

Apache-2.0Auto-check passedResearch & Science

Install Tooluniverse

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/tooluniverse .claude/skills/tooluniverse && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .claude/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/tooluniverse .agents/skills/tooluniverse && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .agents/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/tooluniverse .cursor/skills/tooluniverse && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .cursor/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/tooluniverse

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/tooluniverse .gemini/skills/tooluniverse && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .gemini/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/tooluniverse .github/skills/tooluniverse && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .github/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill tooluniverse -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw tooluniverse --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/tooluniverse .opencode/skills/tooluniverse && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "tooluniverse" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/tooluniverse into .opencode/skills/tooluniverse/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "tooluniverse", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: tooluniverse
GitHub stars: 244
Token cost: ~950 tokens
SKILL.md length: 210 words
Files: 6 (incl. scripts)
Skills in repo: 86
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more

Tasks that involve Bioinformatics
SKILL.md covers Overview, Usage, Parameters (tooluniverse_run.py) and Available Research Workflows…, plus 3 more sections
Runs Python scripts from its folder; calls python3 and pip
Tasks that involve Drug discovery and cheminformatics

What it does

Tooluniverse is an agent skill from lamm-mit/scienceclaw. Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more

Its SKILL.md is about 950 tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts (for example `scripts/tooluniverse_run.py`, `scripts/tooluniverse_search.py` and `setup_tu_skills.py`).

It sits in Research & Science, covering Bioinformatics, Drug discovery and cheminformatics and Clinical and healthcare research. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Bioinformatics
Tasks that involve Drug discovery and cheminformatics
Tasks that involve Clinical and healthcare research

Example prompts

“/tooluniverse”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 4 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
- pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tooluniverse loads about 950 tokens when it runs. Until then it costs about 36 tokens; SKILL.md has 210 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~36
When it runs · the whole SKILL.md, loaded when a task matches: ~950

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 210 words, ~950 tokens.

Download SKILL.mdSave it as .claude/skills/tooluniverse/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.

name: tooluniverse
description: Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more

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:

bash

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

Discover available tools:

bash

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

bash

# 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

bash

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

Files

SKILL.md and 5 other files (scripts) in skills/tooluniverse of lamm-mit/scienceclaw.

SKILL.md
scripts/__pycache__/tooluniverse_run.cpython-313.pyc
scripts/__pycache__/tooluniverse_search.cpython-313.pyc
scripts/tooluniverse_run.py
scripts/tooluniverse_search.py
setup_tu_skills.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Tooluniverse next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Tooluniverse compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Tooluniverse this skilllamm-mit/scienceclaw	244	—	~950	Automated safety check: Pass	Apache-2.0	1 mo ago
Biomedical Analysis Dispatchxjtulyc/MedgeClaw	617	1 repos	~2k	Automated safety check: Pass	None	7 mo ago
Hcls Build Agentaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~885	Automated safety check: Pass	MIT-0	7 days ago
Hcls Get Startedaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~607	Automated safety check: Pass	MIT-0	7 days ago
Genomics Variant Interpretationaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~1.5k	Automated safety check: Pass	MIT-0	7 days ago
Biomnidavila7/claude-code-templates	32k	8 repos	~2.4k	Automated safety check: Notes	MIT	today

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Questions about Tooluniverse

What does Tooluniverse do?

Access 1000+ scientific tools from Harvard's ToolUniverse — bioinformatics, drug discovery, genomics, clinical research, and more. Tooluniverse is an agent skill from lamm-mit/scienceclaw.

When should I use Tooluniverse?

Tooluniverse fits situations like: tasks that involve Bioinformatics; tasks that involve Drug discovery and cheminformatics; tasks that involve Clinical and healthcare research.

How do I install Tooluniverse in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill tooluniverse -a claude-code`. Or copy the skill folder (skills/tooluniverse in lamm-mit/scienceclaw) into .claude/skills/tooluniverse in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill tooluniverse -a codex`. Or copy the skill folder (skills/tooluniverse in lamm-mit/scienceclaw) into .agents/skills/tooluniverse in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill tooluniverse -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tooluniverse, .gemini/skills/tooluniverse, .github/skills/tooluniverse and .opencode/skills/tooluniverse in your project.

What does Tooluniverse need to run?

Going by SKILL.md and its folder, Tooluniverse needs Python for the scripts in its folder and the command-line tools its instructions call (python3 and pip). Our summary lists: Python 3.

Does Tooluniverse access the network?

SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Tooluniverse safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Tooluniverse use?

Tooluniverse is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Tooluniverse use?

About 950 tokens (SKILL.md is roughly 3.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Tooluniverse?

Skills that share tags, products or a category with Tooluniverse: Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars), Hcls Build Agent (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars), Hcls Get Started (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars) and Genomics Variant Interpretation (aws-samples/amazon-bedrock-agents-healthcare-lifesciences, 274 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 86 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Tooluniverse

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

ToolUniverse

Overview

Usage

Run any ToolUniverse tool:

Discover available tools:

Parameters (tooluniverse_run.py)

Available Research Workflows (54+)

Drug Discovery

Genomics & Variants

Omics & Transcriptomics

Disease & Clinical

Proteins & Sequences

Systems Biology

Data Retrieval

Examples

Installation

Notes

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Tooluniverse