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-epigenomics-chromatingit 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-epigenomics-chromatin)<a href="https://agentmods.dev/skills/mims-harvard/tooluniverse/tooluniverse-epigenomics-chromatin"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-epigenomics-chromatin/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-epigenomics-chromatin"><img src="https://agentmods.dev/badge/skills/mims-harvard/tooluniverse/tooluniverse-epigenomics-chromatin.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 | $0.03593 |
| Opus 5 | $0.00052 | $0.01796 |
| Sonnet 5 | $0.00021 | $0.00719 |
| Haiku 4.5 | $0.00010 | $0.00359 |
Grade A, and why
tooluniverse-epigenomics-chromatin 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 12d 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 — 241 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Epigenomics and Chromatin Accessibility Research
NOT for (use other skills instead)
- Methylation array data processing (CpG beta values, differential methylation) -> Use
tooluniverse-epigenomics - RNA-seq differential expression -> Use
tooluniverse-rnaseq-deseq2 - GWAS variant interpretation -> Use
tooluniverse-gwas-snp-interpretation - Variant functional annotation from VCF -> Use
tooluniverse-variant-analysis
Reasoning: Classify the Question First
Before calling any tool, identify which question type you're answering. Each maps to a different tool set.
(a) Which regulatory elements exist at a locus? Use UCSC_get_encode_cCREs (region-based) or SCREEN_get_regulatory_elements (gene-based). Then check ENCODE_get_chromatin_state for ChromHMM annotation and ENCODE_search_chromatin_accessibility for ATAC-seq evidence.
(b) Which TFs bind there? Use ReMap_get_transcription_factor_binding for ChIP-seq experiments. Use jaspar_search_matrices to retrieve binding motifs and check whether the sequence disrupts a known motif.
(c) How does a variant affect regulation? Use RegulomeDB_query_variant for a scored summary. Then build multi-layer evidence: UCSC_get_encode_cCREs (is the variant in a cCRE?), GTEx_get_single_tissue_eqtls (is it an eQTL?), jaspar_search_matrices (does it disrupt a TF motif?). No single layer is sufficient — see the variant reasoning section below.
(d) What genes are regulated by an element? Use GTEx_get_single_tissue_eqtls or GTEx_query_eqtl to find genes whose expression is associated with variants in the element. Use SCREEN_get_regulatory_elements with element_type="PLS"/"pELS"/"dELS" to classify element-to-promoter relationships.
Reasoning: Histone Marks
Use histone mark identity to guide tool queries and interpret results before fetching data.
- H3K4me3 = active promoter. If present without H3K27ac, promoter may be active but not hyperacetylated.
- H3K27ac = active enhancer or promoter. Strong signal = regulatory element is on.
- H3K4me1 = poised or active enhancer. Needs H3K27ac to confirm activity; H3K4me1 alone = poised.
- H3K27me3 = Polycomb repression. Gene is silenced by PRC2.
- H3K9me3 = constitutive heterochromatin. Region is structurally silenced.
- H3K36me3 = transcribed gene body. Confirms active elongation.
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.
- 12d ago First seen · 241 lines · 104 tokens per session scan A 01ad83c1a5cd
tooluniverse-epigenomics-chromatin is a skill published in the GitHub repository mims-harvard/ToolUniverse (1,680 stars, last pushed 2d ago), licensed Apache-2.0. It adds 104 tokens to every session and 3,593 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 2026-08-30.
Other skills, from other repositories
dfam-check
Measure mesh files against Design for Additive Manufacturing (DfAM) rules and report printability findings per process (FDM, SLS, SLA/DLP, metal PBF, MJF). Use when the user asks whether a part is printable, wants overhang/wall-thickness/support analysis of an .stl, .obj, .ply, or .3mf mesh, wants a build-orientation…
nanoresearch-writing
Draft a LaTeX research paper from all previous stage outputs.
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.
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.
astro-dso-doc
Generates a complete, polished HTML documentation page, a processing checklist, an AstroBin post JSON, a PixInsight process icon set (XPSM), AND a ready-to-paste PixInsight project Description field for a deep-sky object (DSO) astrophotography project. Use this skill whenever the user mentions astrophotography, a DSO…
intermediate-outputs
Use this skill when working with circuit discovery in language models, mechanistic interpretability, activation patching, attribution patching, or Layer-wise Relevance Propagation (LRP) for neural network analysis.