Source: https://github.com/aipoch/medical-research-skills

LabArchives Integration

This skill is an Academic Writing workflow built around LabArchives evidence. Its goal is not just API access, but turning authorized ELN material into manuscript-ready writing deliverables.

When to Use

• The user has LabArchives notebook content and needs a Methods draft grounded in recorded procedures.
• The user needs a data availability statement, reproducibility appendix, experiment timeline, or submission support summary based on ELN records.
• The user wants to gather authorized notebook data first, then convert it into academic writing outputs.
• The user needs a deterministic evidence-to-writing workflow instead of freeform summarization.

When Not to Use

• The user asks for unauthorized access to notebooks or other users' data.
• The user wants clinical recommendations, diagnosis, or treatment language.
• The user asks you to fabricate notebook records, timestamps, protocol details, or compliance statements that are not present in the source.
• The user has no authorized export, no notebook metadata, and no textual record to ground the writing output.

Primary Writing Outputs

This skill supports these deliverables:

• Methods Draft Based on notebook entries, protocols, instrument logs, and sample-processing notes
• Data Availability Statement Based on notebook identifiers, repository links, export status, and sharing constraints
• Reproducibility Appendix Based on protocol versions, software environments, parameter logs, and file provenance
• Experiment Timeline Summary Based on dated entries, milestones, and decision points
• Submission Support Note Based on notebook scope, audit trail, and documentation completeness

Authorized Input Sources

Use one or more of:

• exported notebook text or JSON
• manually pasted LabArchives entry content
• protocol summaries
• experiment metadata tables
• authorized backup output from bundled scripts

Optional collection step:

• scripts/setup_config.py

• scripts/notebook_operations.py

• scripts/entry_operations.py

Writing Output Contract

Output A: Methods Draft

Must include:

• study material or sample context
• experimental workflow in chronological order
• instrument / assay / software mentions if present in source
• quality-control or versioning note if present in source
• no invented parameter values

Output B: Data Availability Statement

Must include:

• what data are available
• where they are stored or how they can be requested
• any access restrictions
• relationship to LabArchives or downstream repository

Output C: Reproducibility Appendix

Must include:

• protocol version references
• software or pipeline identifiers if present
• provenance or notebook traceability note
• missing-record warning if the audit trail is incomplete

Output D: Experiment Timeline Summary

Must include:

• dated milestone order
• major protocol transitions
• validation / repeat / deviation points if documented

Workflow

1. Validate authorization and source sufficiency

Confirm:

• the requester has authorized access to the notebook data
• the source contains enough grounded information for the requested writing output

If not, stop and use the refusal template in

## Refusal and Recovery Contract

.

2. Choose the acquisition path

Use direct source text if already available. Prefer this path for speed.

If data must be collected first, use one of the bundled scripts:

python scripts/setup_config.py
python scripts/notebook_operations.py --help
python scripts/entry_operations.py --help

Use

--dry-run

where available before live execution.

3. Normalize notebook evidence

Extract only writing-relevant elements:

• dates
• protocol names and versions
• sample or cohort descriptors
• software / pipeline names
• QC notes
• repository / export details
• compliance or sharing constraints

4. Draft the requested academic writing output

Keep the prose:

• factual
• audit-trail grounded
• publication appropriate
• free of operational noise that does not belong in the manuscript deliverable

5. Run the final writing safety pass

Check that:

• every claim maps back to source evidence
• missing evidence is labeled as missing
• no compliance statement is invented
• no unauthorized identifiers are surfaced

Refusal and Recovery Contract

If the workflow cannot proceed safely, respond with:

Cannot generate the requested LabArchives-based writing output yet.
Reason: <missing authorization / insufficient export / incomplete metadata / unsupported request>
Minimum next step:
- <step 1>
- <step 2>

Use this contract for:

• missing notebook authorization
• no usable export or pasted content
• requests to infer missing protocol details
• requests to expose restricted data

Script Usage Notes

The bundled scripts are supporting collection utilities, not the final output themselves.

• setup_config.py

  : create or validate configuration

• notebook_operations.py

  : list notebooks, plan backups, or perform authorized exports

• entry_operations.py

  : inspect entry-level content or upload artifacts when explicitly needed

If a script path fails:

• report the exact command
• report the exact failure
• continue with direct writing only if enough grounded notebook text is already available

Academic Writing Style Rules

• write in neutral, methods-oriented academic prose
• prefer verifiable chronology over interpretive narrative
• do not overclaim documentation quality if the notebook trail is partial
• clearly distinguish

  documented

  ,

  not documented

  , and

  not provided

Recommended Templates

Use

assets/writing_outputs_template.md

as the default skeleton for the four main writing deliverables.

Deterministic Rules

• keep output headings stable
• do not expose raw credentials, tokens, or private notebook identifiers unless the user explicitly needs authorized internal formatting
• if a timestamp or version is missing, say it is not documented
• treat data availability and reproducibility statements as formal manuscript components, not casual notes

Completion Checklist

• Authorization boundary checked
• Source sufficiency checked
• Requested writing deliverable selected explicitly
• All statements grounded in notebook evidence
• Missing evidence labeled rather than invented