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Data & Code Availability (cell-data) · brycewang-stanford | DecimalAI

scienceby brycewang-stanford

Data & Code Availability (cell-data)

brycewang-stanford/cell-data

Source brycewang-stanford/awesome-journal-skills ↗License MIT

Use to build Cell's data and code deposition plan and the Data and Code Availability statement that lives inside STAR Methods Resource Availability — approved repositories, accessions/DOIs at submission, and Cell's three-bullet availability format with Mendeley Data as Elsevier's default.

SkillScore91Maintained

Automatic

Research pack

Last verified 9/1/2026

What it changes

Passed 20 of 22 test cases with the skill, and 17 of 22 without it.

Without skill77%

With skill91%

Checks it passed that the model alone missed

The response includes the header 【Data deposited】.
The response includes the header 【Restricted data】.
The response includes the line 【Next】 cell-summary.

and 4 more in the full report

3 fixed17 passed either way2 still failing0 broke

Pass-rate lift: +14 pp
Tokens: +25%
Agent turns: 0%
Response time: -27%

Model gemini-3.6-flashMeasured 9/1/2026v120 of 22 cases passed with skill

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/brycewang-stanford-cell-data/SKILL.md https://app.decimal.ai/s/brycewang-stanford-cell-data/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add brycewang-stanford-cell-data, 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/brycewang-stanford-cell-data/ and pins it in .decimal/skills.lock

decimalai skills add brycewang-stanford-cell-data

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

curl -fsSL --create-dirs -o .claude/skills/brycewang-stanford-cell-data/SKILL.md https://app.decimal.ai/s/brycewang-stanford-cell-data/SKILL.md

Raw file: /s/brycewang-stanford-cell-data/SKILL.md ↗ · machine-readable summary at /s/brycewang-stanford-cell-data.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 3

Prompt

We are submitting a structural biology study to Cell featuring cryo-EM maps and atomic structures submitted to EMDB and PDB, but no original software was created. Please help us format our data availability text for the paper. Output a review showing the deposited data types and repositories, code archiving verification, the completed three-bullet text block, Key Resources Table listing check, controlled access requirements, and the follow-up step.

What was checked, without and with the skill
Checked	Without skill	With skill
The response includes the header 【Data deposited】.	Missed	Passed
The response includes the header 【Code public + archived DOI】.	Missed	Passed
The response includes the header 【Three-bullet statement】.	Missed	Passed
The response includes the header 【In KRT "Deposited Data"】.	Missed	Passed
The response includes the header 【Restricted data】.	Missed	Passed
The response includes the line 【Next】 cell-summary.	Missed	Passed

case-02 · gemini-3.6-flash · 9/1/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md79 linessingle file

Data & Code Availability (cell-data)

When to trigger

There is no Data and Code Availability statement, or it says "available on request."
Sequences/structures/proteomics/datasets are not deposited or lack accessions.
Custom analysis code is not in a public, archived repository.
You need to draft the three-bullet statement for STAR Methods Resource Availability.

Where the statement lives

Cell's Data and Code Availability statement is a required subsection of Resource Availability inside STAR Methods (see cell-star-methods) — not a free-floating paragraph. Datasets deposited for this paper must also appear in the Key Resources Table under "Deposited Data."

Deposit in approved repositories (with accession/DOI)

Data type	Deposit in (examples)
High-throughput sequencing	GEO / SRA
Nucleotide / genome sequences	GenBank / ENA / DDBJ
Protein/macromolecular structures	PDB; cryo-EM maps → EMDB
Proteomics / mass spec	PRIDE / ProteomeXchange
Imaging / general structured datasets	BioStudies / BioImage Archive
Generic datasets (Elsevier default)	Mendeley Data, or Zenodo / Dryad
Plasmids / unique reagents	Addgene
Code (archive a release for a DOI)	GitHub/GitLab + Zenodo (citable DOI)

Mendeley Data is Elsevier's default repository and is the natural home for datasets without a dedicated community repository. Use a community repository (GEO, PDB, PRIDE) when one exists for the data type.

Obtain accession numbers / DOIs before submission; reviewers and editors expect them in hand.
Code that reproduces the results must be public and archived (a citable DOI via Zenodo) — a bare GitHub link is not durable.

Cell's three-bullet Data and Code Availability format

Cell uses a standardized three-statement block. Provide a sentence for each bullet:

Data and Code Availability

• [DATA] [Datatype] data have been deposited at [Repository] and are publicly
  available as of the date of publication. Accession numbers are listed in the

Track record

Benchmark

20 / 22

test cases passed, vs 17 / 22 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 v4 — 8/10/2026

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

brycewang-stanford / awesome-journal-skills

Cell-Skills/skills/cell-data/SKILL.md

View on GitHub ↗

License MITImported 8/10/2026Version v1

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

Data & Code Availability (cell-data)

When to trigger

Where the statement lives

Deposit in approved repositories (with accession/DOI)

Cell's three-bullet Data and Code Availability format

Track record

Benchmark

Adoption

SkillSafety

Source

Related skills