Cell Line Profiling (ToolUniverse Claude Skill)

A ToolUniverse agent skill that answers “which cancer cell line should I use to study gene X?” with a ranked, evidence-backed shortlist.

   
Type Claude Skill (one of ToolUniverse’s pre-built agent skills)
Supplier Zitnik Lab, Harvard Medical School
Availability GA — part of the ToolUniverse skills collection (skills/tooluniverse-cell-line-profiling/)
Pricing Free / OSS (Apache-2.0); wraps public resources (DepMap, Cellosaurus, COSMIC, cBioPortal CCLE, Human Protein Atlas, CellMarker, PharmacoDB, SYNERGxDB)
Capabilities Read-only — drives ToolUniverse tool calls; no data writes
Verified works · 2026-08-06
Security cleared · 2026-08-06 — ToolUniverse Apache-2.0, public read-only APIs, no credentials

How to install

This skill calls ToolUniverse tools, so the ToolUniverse MCP server must be installed first (see the ToolUniverse page). Simplest registration:

claude mcp add --transport stdio tooluniverse -- uvx tooluniverse

Then add the skills:

  • Claude Code — install the whole skill collection (the skill resolves as tooluniverse-cell-line-profiling): 
    npx skills add mims-harvard/ToolUniverse
  • Manual / other agents — copy just this skill directory into your skills folder: 
    git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-cell-line-profiling ~/.claude/skills/

    (replace ~/.claude/skills/ with your agent’s skills directory if you are not using Claude Code/Desktop.)

The skill sets disable-model-invocation: true upstream, so invoke it explicitly (e.g. ask Claude to “use the cell-line-profiling skill”) rather than relying on automatic dispatch.

What it does

Runs a five-phase selection workflow:

  1. Identity verification — check the line against Cellosaurus for STR profile and misidentification/contamination flags, and DepMap for tissue, cancer type, and MSI status. Given only a cancer type, it pulls candidate lines and narrows them in later phases.
  2. Molecular profiling — mutations from COSMIC and cBioPortal CCLE, expression from the Human Protein Atlas (which covers only 10 lines), and lineage markers from CellMarker.
  3. Gene dependencies — CRISPR essentiality from DepMap Chronos scores, with < −0.5 as the essentiality cut-off.
  4. Drug sensitivity — IC50 and AAC from PharmacoDB across GDSC, CCLE, and PRISM, plus combination synergy (ZIP scores) from SYNERGxDB.
  5. Ranking — weighted scoring out of 27 (mutation match ×3, co-mutation simplicity ×2, gene dependency ×2, drug data ×1, practical growth factors ×1), returned as ranked recommendations with biological rationale, growth characteristics, and known pitfalls.

Primary use cases: picking a model line for a target-validation experiment, sanity-checking a line already in use, finding lines with a specific mutation background for a drug-sensitivity study.

Notes

It is a reasoning layer over ToolUniverse; without the MCP server registered, the tool calls fail.

Known limitation the skill states upstream: the DepMap API returns metadata only, so per-cell-line Chronos dependency scores come from a bundled depmap_gene_dependency.py script or the depmap.org portal rather than from a live tool call. Expect that phase to need a local script run or a manual portal lookup.

The Cellosaurus identity check in phase 1 is the part worth not skipping — a large fraction of published cancer cell-line work uses misidentified or cross-contaminated lines. Complements the standalone DepMap, cBioPortal, and COSMIC entries, and pairs with Drug Synergy and Drug Target Validation. ToolUniverse ships ~68 such skills; other workflows are catalogued separately.

Sources

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