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-spatial-omics-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-spatial-omics-analysis)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-spatial-omics-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-spatial-omics-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-spatial-omics-analysis"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-spatial-omics-analysis.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 | $0.00097 | $0.03076 |
| Opus 5 | $0.00048 | $0.01538 |
| Sonnet 5 | $0.00019 | $0.00615 |
| Haiku 4.5 | $0.00010 | $0.00308 |
Grade A, and why
tooluniverse-spatial-omics-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 6d 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 — 240 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Spatial Multi-Omics Analysis Pipeline
Comprehensive biological interpretation of spatial omics data. Transforms spatially variable genes (SVGs), domain annotations, and tissue context into actionable biological insights.
KEY PRINCIPLES:
- Report-first approach - Create report file FIRST, then populate progressively
- Domain-by-domain analysis - Characterize each spatial region independently before comparison
- Gene-list-centric - Analyze user-provided SVGs and marker genes with ToolUniverse databases
- Biological interpretation - Go beyond statistics to explain biological meaning of spatial patterns
- Disease focus - Emphasize disease mechanisms and therapeutic opportunities when disease context is provided
- Evidence grading - Grade all evidence as T1 (human/clinical) to T4 (computational)
- Multi-modal thinking - Integrate RNA, protein, and metabolite information when available
- Validation guidance - Suggest experimental validation approaches for key findings
- Source references - Every statement must cite tool/database source
- English-first queries - Always use English terms in tool calls
LOOK UP, DON'T GUESS
When uncertain about any scientific fact, SEARCH databases first (PubMed, UniProt, ChEMBL, ClinVar, etc.) rather than reasoning from memory. A database-verified answer is always more reliable than a guess.
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.
When to Use This Skill
Apply when users:
- Provide spatially variable genes from spatial transcriptomics experiments
- Ask about biological interpretation of spatial domains/clusters
- Need pathway enrichment of spatial gene expression data
- Want to understand cell-cell interactions from spatial data
- Ask about tumor microenvironment heterogeneity from spatial omics
- Need druggable targets in specific spatial regions
- Ask about tissue zonation patterns (liver, brain, kidney)
- Want to integrate spatial transcriptomics + proteomics data
What ships with it
4 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.
- 6d ago First seen · 240 lines · 97 tokens per session scan A ef24bfaa9ede
tooluniverse-spatial-omics-analysis is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,678 stars, last pushed yesterday), licensed Apache-2.0. It adds 97 tokens to every session and 3,076 once invoked, about $0.0005 per session on Opus 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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