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Cancer Cell Line Profiling and Selection · mims-harvard | DecimalAI

scienceby mims-harvard

Cancer Cell Line Profiling and Selection

mims-harvard/tooluniverse-cell-line-profiling

Source mims-harvard/ToolUniverse ↗License Apache-2.0

Cancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.

SkillScore43Maintained

Automatic

Research pack

Last verified 9/7/2026

What it changes

Passed 5 of 12 test cases with the skill, and 2 of 12 without it.

Without skill17%

With skill43%

Checks it passed that the model alone missed

Formats the gene_list parameter as a comma-separated string.
Identifies query as the search parameter for MyGene_query_genes.
Passes compound_name and cell_line_name parameters to PharmacoDB.

and 6 more in the full report

6 fixed4 passed either way13 still failing0 broke

Pass-rate lift: +26 pp
Tokens: +202%
Agent turns: 0%
Response time: -15%

Model gemini-3.6-flashMeasured 9/7/2026v210 of 23 cases passed with skill · 12 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-cell-line-profiling/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-cell-line-profiling/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mims-harvard-tooluniverse-cell-line-profiling, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mims-harvard-tooluniverse-cell-line-profiling/ and pins it in .decimal/skills.lock

decimalai skills add mims-harvard-tooluniverse-cell-line-profiling

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mims-harvard-tooluniverse-cell-line-profiling/SKILL.md https://app.decimal.ai/s/mims-harvard-tooluniverse-cell-line-profiling/SKILL.md

Raw file: /s/mims-harvard-tooluniverse-cell-line-profiling/SKILL.md ↗ · machine-readable summary at /s/mims-harvard-tooluniverse-cell-line-profiling.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 6

Prompt

When querying gene information via MyGene versus searching cell line records in Cellosaurus, what are the respective query parameter names required by each tool's schema?

What was checked, without and with the skill
Checked	Without skill	With skill
Identifies query as the search parameter for MyGene_query_genes.	Missed	Passed
Identifies q as the search parameter for cellosaurus_search_cell_lines.	Passed	Passed

case-12 · gemini-3.6-flash · 9/7/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md269 lines2 filesincludes scripts

Cancer Cell Line Profiling and Selection

Comprehensive profiling of cancer cell lines for experimental model selection. Transforms a query (cancer type, gene, or cell line name) into an actionable report covering identity verification, molecular features, gene dependencies, drug sensitivities, and druggable targets.

KEY PRINCIPLES:

Decision-first - Answer "which cell line should I use?" not "here is all the data"
Multi-source validation - Cross-reference DepMap, Cellosaurus, COSMIC, PharmacoDB
Actionable output - Ranked cell line recommendations with rationale
Practical focus - Include availability, growth characteristics, common pitfalls
Gene-aware - When a gene of interest is given, prioritize lines with relevant mutations/dependencies
Source-referenced - Cite database sources for every claim
English-first queries - Always use English terms in tool calls, even if the user writes in another language

LOOK UP, DON'T GUESS

When uncertain about any scientific fact, SEARCH databases first 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

Apply for: cell line selection by cancer type/gene, cell line profiling, gene dependencies, drug sensitivity queries, cell line comparisons, mutation checks.

Phase 0: Tool Parameter Reference (CRITICAL)

BEFORE calling ANY tool, verify parameters against this table.

Tool	Key Parameters	Notes
`DepMap_search_cell_lines`	`query` (required)	Search by name, e.g., "A549", "MCF"
`DepMap_get_cell_line`	`model_name` OR `model_id`	Name: "A549"; ID: "SIDM00001"
`DepMap_get_cell_lines`	`tissue`, `cancer_type`, `page_size`	Filter by tissue (e.g., "Lung")
`DepMap_get_gene_dependencies`	`gene_symbol` (required), `model_id`	Gene effect scores; negative = essential
`DepMap_search_genes`	`query` (required)	Validate gene symbol in DepMap first
`cellosaurus_search_cell_lines`	`q` (required), `size`	Solr syntax: `id:HeLa`, `ox:9606 AND char:cancer`
`cellosaurus_get_cell_line_info`	`accession` (required, CVCL_ format)	Full cell line record

Track record

Benchmark

5 / 12

test cases passed, vs 2 / 12 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v5 — 9/7/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mims-harvard / ToolUniverse

plugins/tooluniverse/skills/tooluniverse-cell-line-profiling/SKILL.md

View on GitHub ↗

License Apache-2.0Imported 9/7/2026Version v2Bundled 1 file · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

tooluniverse-cell-line-profilingCancer cell-line selection and profiling for experimental model choice. Cross-references DepMap, Cellosaurus, COSMIC, PharmacoDB to deliver identity verification, mutation/CNV profile, gene dependencies, drug sensitivities, and druggable targets. Use to answer 'which cell line should I use for studying gene X?' or 'is this cell line a good model for cancer Y?'. Outputs ranked recommendations with rationale, growth characteristics, and known pitfalls.Near-identical description-26 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

Ready to supercharge your AI agents?

See it in action

What's inside

Cancer Cell Line Profiling and Selection

LOOK UP, DON'T GUESS

COMPUTE, DON'T DESCRIBE

When to Use

Phase 0: Tool Parameter Reference (CRITICAL)

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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