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-stem-cell-organoidgit 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-stem-cell-organoid)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-stem-cell-organoid"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-stem-cell-organoid/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-stem-cell-organoid"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-stem-cell-organoid.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 | $0.00064 | $0.02049 |
| Opus 5.5 | $0.00026 | $0.00820 |
| Sonnet 5.5 | $0.00013 | $0.00410 |
| Haiku 4.5 | $0.00006 | $0.00205 |
Grade A, and why
tooluniverse-stem-cell-organoid 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 — 134 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Stem Cell & Organoid Research
Pipeline for investigating stem cell biology, iPSC characterization, organoid models, and cell differentiation using ToolUniverse tools.
Reasoning Strategy
Stem cell differentiation follows developmental biology — to make any target cell type from iPSCs, the protocol must mimic the embryonic signaling pathway that generates that cell type in vivo. For neural induction: inhibit BMP and TGF-beta (dual SMAD inhibition). For cardiomyocytes: activate WNT then inhibit WNT. For pancreatic beta cells: activate Activin/Nodal → FGF → Notch inhibition → BMP in sequence. The order and timing of growth factors matters critically — adding BMP4 during neural induction will redirect cells toward mesoderm. Mouse and human stem cells differ in their signaling requirements (LIF/STAT3 for mouse naive pluripotency; FGF/ERK for human primed pluripotency), so protocols are not interchangeable. Organoids recapitulate some but not all organ features — always assess maturation state (fetal vs. adult gene expression) before drawing disease-relevance conclusions.
LOOK UP DON'T GUESS: Do not assume which markers define a target cell type or which signaling pathway drives differentiation — query CellMarker_search_by_cell_type for markers and kegg_search_pathway for the relevant pathway. Do not assume organoid fidelity; look up published CellxGene or HCA atlas data for comparison.
Key principles:
- Marker-based identity — stem cell identity is defined by marker expression profiles (OCT4, SOX2, NANOG for pluripotency)
- Differentiation is a trajectory — not a binary state; analyze intermediate progenitor stages
- Organoid ≠ organ — organoids recapitulate some but not all organ features; always note limitations
- Species matters — mouse and human stem cells differ in signaling requirements
- Evidence grading — T1: validated in clinical iPSC study, T2: functional assay (teratoma, engraftment), T3: marker expression only, T4: computational prediction
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 · 134 lines · 64 tokens per session scan A a9dc7b7d2265
tooluniverse-stem-cell-organoid 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 2,049 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.
Other skills, from other repositories
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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.