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-systems-biologygit 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-systems-biology)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-systems-biology"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-systems-biology/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-systems-biology"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-systems-biology.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- 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 | $0.00072 | $0.06883 |
| Opus 5.5 | $0.00029 | $0.02753 |
| Sonnet 5.5 | $0.00014 | $0.01377 |
| Haiku 4.5 | $0.00007 | $0.00688 |
Grade A, and why
tooluniverse-systems-biology scanned grade A with 1 finding 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
`ReactomeInteractors_get_protein_interactors`, `ReactomeInteractors_get_entity_pathways`, `ReactomeInteractors_search_entity` (`reactome_interactors_tools.json`) — **all 3 tools currently return HTTP 521 on every call**, How it starts
The opening of the file, as written. The whole thing — 368 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Systems Biology & Pathway Analysis
Comprehensive pathway and systems biology analysis integrating multiple curated databases to provide multi-dimensional view of biological systems, pathway enrichment, and protein-pathway relationships.
When to Use This Skill
Triggers:
- "Analyze pathways for this gene list"
- "What pathways is [protein] involved in?"
- "Find pathways related to [keyword/process]"
- "Perform pathway enrichment analysis"
- "Map proteins to biological pathways"
- "Find computational models for [process]"
- "Systems biology analysis of [genes/proteins]"
Use Cases:
- Gene Set Analysis: Identify enriched pathways from RNA-seq, proteomics, or screen results
- Protein Function: Discover pathways and processes a protein participates in
- Pathway Discovery: Find pathways related to diseases, processes, or phenotypes
- Systems Integration: Connect genes → pathways → processes → diseases
- Model Discovery: Find computational systems biology models (SBML)
- Cross-Database Validation: Compare pathway annotations across multiple sources
COMPUTE, DON'T DESCRIBE
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
Domain Reasoning: Enrichment vs Causation
Pathway analysis answers: which biological processes are enriched in my gene list? But enrichment is not causation. A pathway being enriched means your gene list overlaps it more than expected by chance. Ask: is the enrichment driven by a few hub genes, or by many genes distributed across the pathway? A pathway with 3 input genes but 200 annotated members is less informative than one where 15 of 40 members are in your list.
LOOK UP DON'T GUESS: pathway membership, gene-to-pathway assignments, and enrichment statistics. Do not assume a gene is in a pathway — use Reactome, KEGG, or Enrichr to verify. Pathway databases disagree on membership; cross-validate key findings across at least two sources.
What ships with it
6 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 · +97 lines 7f8c1810fdca
- 1mo ago First seen · 271 lines · 72 tokens per session scan A a3f84e17b2da
tooluniverse-systems-biology is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 72 tokens to every session and 6,883 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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apache-iv-score
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