ToolUniverse is a collection of tools, interfaces, and supporting components for building AI systems that perform scientific work. It is for developers creating AI scientist agents that use APIs, databases, machine-learning tools, and domain-specific utilities. The catalogue includes skills, commands, an MCP server, an agent, and a hook for working with the ecosystem.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add mims-harvard/ToolUniverse --skill tooluniverse-metabolomicsgit clone --depth 1 https://github.com/mims-harvard/ToolUniverseWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk warn
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00071 | $0.03050 |
| Opus 5.5 | $0.00028 | $0.01220 |
| Sonnet 5.5 | $0.00014 | $0.00610 |
| Haiku 4.5 | $0.00007 | $0.00305 |
Grade A, and why
tooluniverse-metabolomics scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 296 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Metabolomics Research
Comprehensive metabolomics research skill that identifies metabolites, analyzes studies, and searches metabolomics databases. Generates structured research reports with annotated metabolite information, study details, and database statistics.
Use Case
Use this skill when asked to:
- Identify or annotate metabolites (HMDB IDs, chemical properties, pathways)
- Retrieve metabolomics study information from MetaboLights or Metabolomics Workbench
- Search for metabolomics studies by keywords or disease
- Analyze metabolite profiles or datasets
- Generate comprehensive metabolomics research reports
Example queries:
- "What is the HMDB ID and pathway information for glucose?"
- "Get study details for MTBLS1"
- "Find metabolomics studies related to diabetes"
- "Analyze these metabolites: glucose, lactate, pyruvate"
Databases Covered
Primary metabolite databases:
- HMDB (Human Metabolome Database): 220,000+ metabolites with structures, pathways, and biological roles
- MetaboLights: Public metabolomics repository with thousands of studies
- Metabolomics Workbench: NIH Common Fund metabolomics data repository
- FooDB: Food chemical-constituent database — use
FooDB_get_compound(paramfdb_id, e.g."FDB000004") for a food compound's structure plus HMDB/KEGG/PubChem/ChEBI cross-references; ideal for food-metabolomics annotation - PubChem: Chemical properties and bioactivity data (fallback)
Research Workflow
The skill executes a 4-phase analysis pipeline:
Phase 1: Metabolite Identification & Annotation
For each metabolite in the input list:
- Search HMDB by metabolite name
- Retrieve HMDB ID, chemical formula, molecular weight
- Get detailed metabolite information (description, pathways)
- Fallback to PubChem for CID and chemical properties if HMDB unavailable
Phase 2: Study Details Retrieval
For provided study IDs:
- Detect database type (MTBLS = MetaboLights, ST = Metabolomics Workbench)
- Retrieve study metadata (title, description, organism, status)
- Extract experimental design and data availability
What ships with it
12 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- .env.template 499 B
- diabetes_analysis.py 1.7 KB runs code
- example1_metabolites.md 722 B
- example2_study.md 631 B
- example3_search.md 861 B
- python_implementation.py 10 KB runs code
- QUICK_START.md 12 KB
- scripts/metabolism_ref.py 9.5 KB runs code
- test1_metabolites.md 1011 B
- test2_study.md 753 B
- test3_search.md 859 B
- test4_comprehensive.md 1.6 KB
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 296 lines · 71 tokens per session scan A 9ddba689efeb
tooluniverse-metabolomics is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 71 tokens to every session and 3,050 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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