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-precision-medicine-stratificationgit 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-precision-medicine-stratification)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-precision-medicine-stratification"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-precision-medicine-stratification/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-precision-medicine-stratification"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-precision-medicine-stratification.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 | $0.00067 | $0.02826 |
| Opus 5.5 | $0.00027 | $0.01130 |
| Sonnet 5.5 | $0.00013 | $0.00565 |
| Haiku 4.5 | $0.00007 | $0.00283 |
Grade A, and why
tooluniverse-precision-medicine-stratification 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 — 216 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Precision Medicine Patient Stratification
Transform patient genomic and clinical profiles into actionable risk stratification, treatment recommendations, and personalized therapeutic strategies.
Reasoning Before Searching
Stratification means splitting patients into groups that respond differently to a treatment or have different prognoses. Ask these questions before running any tools:
- What molecular feature predicts response? Candidates: somatic mutation (e.g., EGFR L858R), germline variant (e.g., BRCA1 LoF), expression level (e.g., HER2 overexpression), germline pharmacogenomic variant (e.g., CYP2C19 PM), or composite biomarker (e.g., TMB-H + MSI-H).
- Is the predictive feature actionable? Knowing it must change treatment — either the drug choice, dose, or monitoring plan. A variant with prognostic value but no therapeutic consequence is not a stratification biomarker.
- What is the evidence level for the stratifier? FDA-approved companion diagnostic (T1) vs. exploratory (T4) changes how much weight to place on the finding.
Route to the correct Phase 3 path BEFORE running Phase 2 tools — cancer, metabolic, CVD, rare disease, and autoimmune pipelines require different stratifiers.
LOOK UP DON'T GUESS: Never assume a variant is pathogenic, never assume a gene is relevant to a disease, never assign metabolizer status without PharmGKB or CPIC evidence.
KEY PRINCIPLES:
- Report-first - Create report file FIRST, then populate progressively
- Disease-specific logic - Cancer vs metabolic vs rare disease pipelines diverge at Phase 3
- Multi-level integration - Germline + somatic + expression + clinical data layers
- Evidence-graded - Every finding has an evidence tier (T1-T4)
- Quantitative output - Precision Medicine Risk Score (0-100)
- Source-referenced - Every statement cites the tool/database source
- English-first queries - Always use English terms in tool calls
Reference files (same directory):
TOOLS_REFERENCE.md- Tool parameters, response formats, phase-by-phase tool listsSCORING_REFERENCE.md- Scoring matrices, risk tiers, pathogenicity tables, PGx tablesREPORT_TEMPLATE.md- Output report template, treatment algorithms, completeness requirementsEXAMPLES.md- Six worked examples (cancer, metabolic, NSCLC, CVD, rare, neuro)QUICK_START.md- Sample prompts and output summary
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.
- 1mo ago First seen · 216 lines · 67 tokens per session scan A 8b1d6d749f34
tooluniverse-precision-medicine-stratification is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 67 tokens to every session and 2,826 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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