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-metabolomics-analysisgit 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-analysis)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics-analysis/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-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-metabolomics-analysis.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 | $0.00064 | $0.03433 |
| Opus 5.5 | $0.00026 | $0.01373 |
| Sonnet 5.5 | $0.00013 | $0.00687 |
| Haiku 4.5 | $0.00006 | $0.00343 |
Grade A, and why
tooluniverse-metabolomics-analysis 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 10d 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 — 222 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Metabolomics Analysis
Comprehensive analysis of metabolomics data from metabolite identification through quantification, statistical analysis, pathway interpretation, and integration with other omics layers.
Domain Reasoning
Metabolomics quantification depends critically on normalization. Total ion current (TIC) normalization corrects for sample-loading variation and works well for global abundance changes; internal standard normalization is more accurate for targeted analysis where specific metabolite concentrations matter. Missing values in a peak table may reflect signal below the detection limit — not true absence — and should be imputed or handled explicitly rather than treated as zero. Failing to account for batch effects across instrument runs is a frequent source of spurious differential metabolites.
LOOK UP DON'T GUESS
- Metabolite identities: use
Metabolite_searchandMetabolite_get_infoto confirm names, CIDs, and HMDB IDs; never assume identity from m/z alone. - Pathway memberships: query KEGG, MetaCyc, or Reactome tools; do not list pathways from memory.
- Disease associations: retrieve from CTD via
Metabolite_get_diseases; do not infer clinical relevance without database evidence. - CV thresholds and QC criteria: apply the values defined in this workflow (CV < 30%, blank ratio > 3x); do not override with guesses.
When to Use This Skill
Triggers:
- User has metabolomics data (LC-MS, GC-MS, NMR)
- Questions about metabolite abundance or concentrations
- Differential metabolite analysis requests
- Metabolic pathway analysis
- Multi-omics integration with metabolomics
- Metabolic biomarker discovery
- Flux balance analysis or metabolic modeling
- Metabolite-enzyme correlation
Example Questions:
- "Analyze this LC-MS metabolomics data for differential metabolites"
- "Which metabolic pathways are dysregulated between conditions?"
- "Identify metabolite biomarkers for disease classification"
- "Correlate metabolite levels with enzyme expression"
- "Perform pathway enrichment for differential metabolites"
- "Integrate metabolomics with transcriptomics data"
What ships with it
2 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.
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.
- 10d ago Changed · +23 lines 413fd060eb11
- 1mo ago First seen · 199 lines · 64 tokens per session scan A f992835a6350
tooluniverse-metabolomics-analysis is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 64 tokens to every session and 3,433 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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