Agent Skills
› brycewang-stanford/Awesome-Journal-Skills
› molcell-data
molcell-data
GitHub用于构建Molecular Cell论文的数据与代码可用性声明，指导数据存入GEO/PDB/PRIDE等指定库获取 accession，规范STAR Methods中的标准化表述格式。
Trigger Scenarios
缺少数据与代码可用性声明或仅写“按需提供”
测序、结构或蛋白质组学数据未存档或缺乏登录号
自定义分析代码未存入公开归档仓库
需要起草STAR Methods资源可用性的标准声明
Install
npx skills add brycewang-stanford/Awesome-Journal-Skills --skill molcell-data -g -y
SKILL.md
Frontmatter
{
"name": "molcell-data",
"description": "Use to build Molecular Cell's data and code deposition plan and the Data and Code Availability statement inside STAR Methods Resource Availability — approved repositories (GEO, PDB\/EMDB, PRIDE), accessions\/DOIs at submission, and Cell Press's standardized availability format with Mendeley Data as Elsevier's default."
}
Data & Code Availability (molcell-data)
When to trigger
- There is no Data and Code Availability statement, or it says "available on request."
- Sequencing / structures / proteomics / datasets are not deposited or lack accessions.
- Custom analysis code is not in a public, archived repository.
- You need to draft the standardized statement for STAR Methods Resource Availability.
Where the statement lives
Molecular Cell's Data and Code Availability statement is a required subsection of Resource Availability inside STAR Methods (see molcell-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 (ChIP/RNA/ATAC/CLIP-seq) | GEO / SRA |
| Nucleotide / genome sequences | GenBank / ENA / DDBJ |
| Macromolecular structures | PDB |
| Cryo-EM maps (and half-maps) | EMDB (map) + PDB (model) |
| Crystallography | PDB (coordinates + structure factors) |
| Proteomics / mass spec / cross-linking MS | PRIDE / ProteomeXchange (+ jPOST where used) |
| NMR | BMRB + PDB |
| 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 for datasets without a dedicated community repository. Prefer a community repository (GEO, PDB/EMDB, PRIDE) when one exists for the data type — Molecular Cell's molecular focus means most primary data have one.
- Obtain accession numbers / DOIs before submission; reviewers and editors expect them in hand, and for structures they will check map-model fit against the deposited entry.
- Code that reproduces the analysis must be public and archived (a citable DOI via Zenodo) — a bare GitHub link is not durable.
Cell Press Data and Code Availability format
Cell Press uses a standardized statement. Provide a sentence for each item:
Data and Code Availability
• [DATA] The [datatype] data generated in this study have been deposited at
[GEO / PDB+EMDB / PRIDE] and are publicly available as of the date of
publication. Accession numbers are listed in the Key Resources Table. /
This paper analyzes existing, publicly available data [accessions in KRT].
• [CODE] All original code has been deposited at [Zenodo/Mendeley Data] and is
publicly available as of the date of publication. DOIs are listed in the Key
Resources Table. / This paper does not report original code.
• [ADDITIONAL] Any additional information required to reanalyze the data
reported in this paper is available from the Lead Contact upon request.
Each item must be addressed even if the answer is "this paper does not report…". Restricted human/clinical data must state the controlled-access procedure and the controlling body.
Structure-specific deposition (Molecular Cell-heavy)
- Cryo-EM: deposit the map (and typically half-maps and mask) at EMDB and the model at PDB; report the resolution and the FSC threshold used.
- X-ray: deposit coordinates and structure factors at PDB.
- Validation reports should be generatable from the deposited entries — reviewers may request them.
Materials & ethics cross-links
- Unique materials sharing belongs in Materials Availability (
molcell-star-methods); use Addgene/MTA and state how. - Ethics approvals (IRB/IACUC, consent, permits) belong in Experimental Model and Subject Details.
- Identify key reagents with RRIDs in the Key Resources Table.
Output format
【Data deposited】 type → repository → accession/DOI (list each) | gaps
【Structures】 EMDB/PDB (map+model) or PDB (coords+SF)? resolution/FSC stated?
【Code public + archived DOI】 yes/no (repo + Zenodo/Mendeley DOI)
【Statement】 DATA ☐ / CODE ☐ / ADDITIONAL ☐ — all drafted?
【In KRT "Deposited Data"】 accessions listed? yes/no
【Restricted data】 controlled-access procedure stated where needed?
【Next】 molcell-summary
Anti-patterns
- Do not write "available on request" for the primary data behind the figures.
- Do not deposit a structure model without its map/structure factors.
- Do not link only to a personal/lab website — use an archival repository with a DOI.
- Do not forget to mirror accessions into the Key Resources Table.
- Do not submit without accession numbers/DOIs in hand.
Confirm repository requirements and the exact availability wording against current Cell Press / STAR Methods guidelines.
Version History
- 9f86f09 Current 2026-07-19 17:04
