Generate Scientific Method Section

Overview

generate_scientific_method_section closes the LabOS "from bench to paper" loop by automatically drafting the Methods section of a SCI manuscript directly from machine-readable experiment records. It ingests heterogeneous upstream artifacts — LabOS skill execution logs, structured JSON from video analysis pipelines, protocols.io or Benchling ELN entries, reagent inventory metadata, and statistical analysis outputs — extracts every parameter, reagent, instrument, and procedural decision, and synthesizes them into complete, journal-ready Methods prose following IMRAD conventions. Output is LaTeX or Markdown with numbered subsections, in-text citations formatted for a target journal style, and a reproducibility checklist, eliminating the most time-consuming transcription step between bench work and manuscript submission.

When to Use This Skill

Use this skill when any of the following conditions are present:

• Post-experiment write-up: An experiment has been completed and its execution records (LabOS logs, ELN entries, video analysis JSONs) are available; the next step is to draft the Methods section without manually transcribing every parameter and reagent.
• LabOS pipeline completion: A multi-skill LabOS execution chain (extract_experiment_data_from_video → analyze_lab_video_cell_behavior → generate_cell_analysis_charts) has finished and the agent must now document what was done in manuscript form.
• Protocol-to-manuscript conversion: A structured protocols.io or Benchling protocol was followed (with or without deviations logged by protocol_video_matching) and must be converted from step-list format to flowing SCI-style prose.
• Compliance-driven documentation: A regulated workflow (GLP/GMP, clinical research) requires that the exact executed procedure — including any deviations — be documented in a standardized textual format for submission or audit.
• Reproducibility package preparation: A paper is being submitted with a reproducibility requirement (Nature Methods, eLife, PLOS ONE) and the Methods section must contain every parameter needed to fully replicate the experiment.
• Multi-experiment manuscript: Several related experiments were run across different sessions; their individual logs must be merged into a coherent, unified Methods section with appropriate cross-references.
• Revision round: A reviewer requests more detail in the Methods; the original execution logs are mined to surface omitted parameters, instrument settings, or statistical choices.
• Collaborative lab writing: A trainee performed the experiment; the skill auto-drafts the Methods from their ELN entry so a senior author can review and annotate rather than write from scratch.