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-regulatory-variant-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-regulatory-variant-analysis)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-regulatory-variant-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-regulatory-variant-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-regulatory-variant-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-regulatory-variant-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- 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 | $0.00104 | $0.05089 |
| Opus 5.5 | $0.00042 | $0.02036 |
| Sonnet 5.5 | $0.00021 | $0.01018 |
| Haiku 4.5 | $0.00010 | $0.00509 |
Grade A, and why
tooluniverse-regulatory-variant-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 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 — 286 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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.
Regulatory Variant Analysis Skill
Systematic regulatory variant interpretation: discover trait associations from GWAS, map eQTL effects, annotate chromatin context, assess regulatory element overlap, predict direct sequence-level effects with AlphaGenome/AlphaGenome Atlas, and produce evidence-graded functional impact predictions for non-coding variants.
When to Use
- "What GWAS associations exist for rs12913832?"
- "Find eQTLs for the APOE locus in brain tissue"
- "What regulatory elements overlap this variant region?"
- "Which SNPs are associated with type 2 diabetes from GWAS?"
- "Is this intronic variant in an active enhancer?"
- "What is the RegulomeDB score for rs429358?"
- "Find ENCODE histone marks at the BRCA1 promoter region"
- "Map trait ontology terms for 'blood pressure' to EFO IDs"
- "This variant has no GWAS/eQTL/ENCODE hits at all — does a sequence model predict any effect?"
- "Scan this candidate regulatory region to find which single base change matters most"
NOT for (use other skills instead):
- Coding variant pathogenicity -> Use
tooluniverse-variant-interpretation - Full clinical variant classification (ACMG) -> Use
tooluniverse-variant-interpretation - Gene-disease associations (not variant-specific) -> Use
tooluniverse-gene-disease-association - Pharmacogenomic variant annotation -> Use
tooluniverse-pharmacogenomics - Epigenomics data processing (BED/narrowPeak files) -> Use
tooluniverse-epigenomics
Non-Coding Variant Impact Reasoning
When evaluating a non-coding variant, build evidence across five questions. The first four are annotation-based (what's already known to be at this position, in this population); the fifth is model-based (what the sequence itself predicts, whether or not anything is annotated there yet) — they answer different questions and should corroborate, not substitute for, each other.
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 Changed · +82 lines · +20 tokens per session 74eb9fcc0315
- 1mo ago First seen · 204 lines · 84 tokens per session scan A 649ba8133ef6
tooluniverse-regulatory-variant-analysis is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,744 stars, last pushed yesterday), licensed Apache-2.0. It adds 104 tokens to every session and 5,089 once invoked, about $0.0004 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.
Other skills, from other repositories
ai-agent-tool-routing
Use when designing or reviewing an AI agent tool registry or MCP router: document parameter schemas, caller authorization, execution limits, replay-safe retries and verification evidence.
nanoresearch-writing
Draft a LaTeX research paper from all previous stage outputs.
construct-toy-examples
Generate and analyze simpler examples that satisfy both the assumptions and the conclusion of a theorem statement or subgoal. Use when you are stuck in reasoning and need simpler examples to regain traction, or when you want to see where the assumptions take effect and gain intuition.
obtain-immediate-conclusions
Derive immediate mathematical consequences from a theorem statement or subgoal. Use when starting a new problem, branch, or subgoal, or when cheap progress or a cleaner reformulation is needed before deeper proof search.
clinical-research-analysis-framework
Guided workflow for statistical and ML analysis of clinical data. Use when planning or executing research analyses on MIMIC, eICU, or similar EHR data. Ensures methodological rigor through structured consultation, assumption checking, and stepwise execution with audit trails.
apache-iv-score
Calculate APACHE IV (Acute Physiology and Chronic Health Evaluation IV) score for ICU mortality prediction. Use for severity assessment, hospital mortality prediction, ICU benchmarking, or case-mix adjustment. eICU has pre-computed scores; MIMIC-IV requires custom implementation with diagnosis mapping challenges.