Generate Scientific Method Section

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.

Core Capabilities

1. Multi-Source Record Ingestion & Provenance Extraction

Parses all available upstream artifacts to build a unified experiment provenance graph before writing:

• LabOS skill call chain logs: JSON execution traces listing each invoked skill, its input parameters, output summaries, timestamps, and agent decisions — extracted as a structured timeline of experimental events
• Video analysis JSON (extract_experiment_data_from_video, analyze_lab_video_cell_behavior): Timeseries data, detected events (volume additions, color transitions, deviation flags), quantitative metrics, and extraction parameters all interpreted as ground-truth records of what was physically done
• Protocol sources (protocolsio-integration, benchling-integration): Protocol step text, reagent lists with catalog numbers, equipment specifications, and version/DOI — used as the expected procedure baseline; deviations recorded by protocol_video_matching are merged as amendments
• ELN entries: Free-text notebook entries, attached files, reagent lot numbers, and instrument calibration records parsed from Benchling, LabArchive, or plain Markdown ELN exports
• Statistical analysis outputs (statistical-analysis, pymc, statsmodels): Test names, degrees of freedom, p-values, effect sizes, and software versions extracted from analysis logs and formatted into a Statistical Analysis subsection
• Reagent / inventory metadata: Manufacturer, catalog number, lot number, purity, and CAS number for every reagent identified in the record; cross-referenced against common supplier databases (Sigma-Aldrich, Thermo Fisher, Abcam) to auto-complete missing catalog details
• Conflict resolution: When the executed record diverges from the reference protocol (detected by protocol_video_matching), the skill reports the deviation inline in the Methods text as a parenthetical amendment rather than silently adopting either source

2. Methods Section Structure & Subsection Decomposition

Organizes extracted information into the standard Methods architecture for the target field:

Default subsection scaffold (cell biology / biochemistry):

• Field adaptation: Scaffold adjusts for target field — molecular biology adds \subsection{Cloning and Mutagenesis}, animal studies add \subsection{Animal Housing and Ethics}, clinical studies add \subsection{Patient Cohort and IRB Approval}
• Subsection merging: Short subsections (< 3 sentences each) are intelligently merged to avoid fragmented prose
• Ordered narrative: Within each subsection, events are ordered chronologically by timestamp from the execution log, not by protocol step number, ensuring the text reflects what was actually done

3. SCI-Grade Prose Generation

Converts structured records into flowing scientific prose meeting journal standards:

• Voice and tense: Passive voice, past tense throughout ("Cells were seeded…", "Fluorescence images were acquired…", "Statistical significance was defined as…") — consistent with Methods convention across all major journals
• Precision without redundancy: Exact numeric values for all parameters (temperature, time, concentration, centrifuge speed, volume) with SI units and ± tolerances where applicable; avoids vague language ("briefly", "overnight") by substituting exact values from logs
• Sentence variety: Combines simple declarative sentences for procedure steps with compound sentences for contextual justification (e.g., "…to minimize photobleaching, images were acquired at 10% laser power"); avoids bullet-list prose
• Defined abbreviations: First use of every abbreviation is spelled out and defined inline (DMEM, DAPI, PBS, etc.) following journal convention
• Forward/backward cross-references: Figures, tables, and supplementary materials referenced at appropriate points ("as described in Supplementary Methods S1", "representative images shown in Figure 2B")
• Reagent citation format: Reagents cited in parentheses inline per journal style — e.g., (Lipofectamine 3000; Thermo Fisher Scientific, L3000015) — with style switchable per target journal

4. LaTeX & Markdown Formatting

Emits manuscript-ready formatted output:

LaTeX output (default):

\subsection{Cell Culture}
HeLa cells (ATCC CCL-2) were maintained in Dulbecco's modified Eagle's medium
(DMEM; Thermo Fisher Scientific, 11965092) supplemented with 10\% fetal bovine
serum (FBS; Sigma-Aldrich, F2442, lot 22A0145) and 1\% penicillin--streptomycin
(Thermo Fisher Scientific, 15140122) at 37\,\textdegree{}C in a humidified
atmosphere of 5\% CO\textsubscript{2}. Cells were passaged every 3--4 days and
tested negative for mycoplasma contamination by PCR (Lonza, LT07-701) prior to
use. All experiments were performed between passages 5 and 20.

\subsection{Wound-Healing Assay}
For scratch assays, $5 \times 10^{4}$ cells were seeded into 24-well plates
(Corning, 3524) and grown to confluency over 24\,h. A uniform scratch was
introduced across the cell monolayer using a 200\,\textmu{}L pipette tip, and
wells were washed twice with PBS to remove detached cells. Medium was replaced
with serum-free DMEM supplemented with 10\,ng\,mL\textsuperscript{-1} EGF
(Sigma-Aldrich, SRP3027). Phase-contrast time-lapse images were acquired every
30\,min for 24\,h using a Zeiss Axio Observer~7 inverted microscope equipped
with a 10\texttimes{}/0.3\,NA objective and an Axiocam~702 camera. Wound closure
was quantified using the \texttt{extract\_experiment\_data\_from\_video} pipeline
(LabOS v2.1), with migration front positions determined by automated edge
detection as described below.

• Environment support: \subsection{}, \subsubsection{}, \paragraph{}; inline math ($...$); chemical formulas (CO\textsubscript{2}); unit formatting (\,\textmu{}L, \,\textdegree{}C); reagent catalog numbers in \texttt{}
• Citation integration: Compatible with BibTeX (\cite{key}), natbib (\citep{} / \citet{}), and author-number styles; citation keys auto-generated from author + year + first-word when a reference list is supplied
• Journal style presets: Nature family (Methods after main text, brief style), Science (Methods in supplement), Cell (STAR Methods format with Key Resources Table), PLOS ONE, eLife — each preset adjusts subsection hierarchy and prose density
• Markdown output: GitHub-flavored Markdown for ELN embedding, Notion, or Benchling; uses ## / ### headings; reagents in bold with catalog numbers; code blocks for software parameters
• STAR Methods / Key Resources Table: For Cell-family journals, auto-generates the structured Key Resources Table (reagents, antibodies, software, deposited data) alongside the prose Methods

5. Reproducibility & Compliance Checklist

Audits the generated Methods section against reproducibility standards and flags gaps:

• Reproducibility score: Counts how many of the 25 MIQE / ARRIVE / MIAME / general reproducibility criteria are satisfied by the draft; reports as n/25 with a list of missing items
• Missing parameter detection: Identifies parameters present in execution logs but absent from the draft (e.g., centrifuge rotor model, antibody dilution, software version) and either inserts them or flags them for manual addition
• RRID compliance: Checks that all cell lines, antibodies, organisms, and key reagents have an RRID (Research Resource Identifier) cited; inserts known RRIDs automatically from the SciCrunch database lookup or flags unknown ones
• Software version citation: Ensures every software tool mentioned has a version number and citation (DOI or PMID); flags tools cited without version (e.g., "analyzed using ImageJ" → flags missing version and suggests \cite{Schindelin2012})
• Statistical reporting completeness: Verifies that the Statistical Analysis subsection reports test name, software, version, sample sizes (n), exact p-values or ranges, effect sizes, and multiple-comparison correction method
• Ethics and consent statements: For animal or human subject experiments, flags absence of ethics approval number or IRB statement

6. Deviation & Amendment Documentation

Ensures the Methods text accurately reflects what was executed, not just what was planned:

• Protocol deviation integration: Deviations logged by protocol_video_matching (e.g., WRONG_PARAMETER: 200 µL PBS used instead of 250 µL) are incorporated as inline amendments: "PBS wash volume was 200 µL (protocol specifies 250 µL) due to reagent availability."
• Deviation severity gating: MINOR deviations are noted parenthetically; MAJOR or CRITICAL deviations trigger a dedicated \paragraph{Procedural Amendments} with explicit justification placeholder
• Conditional branching documentation: If the protocol included decision branches (e.g., "if pellet not visible, centrifuge again") and the branch was taken, the executed path is described; untaken branches are omitted
• Reproducibility note: When a deviation affects reproducibility, the skill appends a sentence recommending that readers follow the original protocol reference for strict replication

Usage Examples

Example 1 — Full Methods Section from LabOS Pipeline Execution Log

Natural language trigger:

"We just finished the scratch assay pipeline run. Generate the full Methods section in LaTeX for our Cell Reports submission."

Input artifacts:

skill_chain_log:    "labos_run_2026-03-06_scratch_assay.json"
video_analysis:     "results/scratch_assay_A549_EGF_24h.json"      # from extract_experiment_data_from_video
cell_analysis:      "results/cell_behavior_A549_EGF_24h.json"       # from analyze_lab_video_cell_behavior
protocol_source:    "protocols.io:dx.doi.org/10.17504/protocols.io.scratch-v2"
eln_entry:          "benchling://entry/etr_abc123"
target_journal:     "Cell Reports"
output_format:      "latex"

Generated LaTeX output (excerpt):

\section*{STAR Methods}

\subsection*{Key Resources Table}
% [auto-generated Key Resources Table: reagents, cell lines, software, datasets]

\subsection*{Experimental Model and Subject Details}

\paragraph{Cell Lines}
A549 human lung adenocarcinoma cells (ATCC CCL-185; RRID:CVCL\_0023) were
maintained in F-12K medium (ATCC, 30-2004) supplemented with 10\% fetal bovine
serum (Sigma-Aldrich, F2442, lot 22A0145) at 37\,\textdegree{}C and 5\%
CO\textsubscript{2}. Cells were confirmed mycoplasma-negative (Lonza LT07-701)
and used between passages 4 and 18.

\subsection*{Method Details}

\paragraph{Wound-Healing Migration Assay}
For migration assays, $2 \times 10^{5}$ A549 cells were seeded in 24-well plates
(Corning, 3524) and cultured for 24\,h to confluency. A linear scratch was
introduced with a sterile 200\,\textmu{}L pipette tip, after which wells were
washed twice with phosphate-buffered saline (PBS; Thermo Fisher Scientific,
10010023) to remove debris. Cells were treated with 10\,ng\,mL\textsuperscript{-1}
recombinant human EGF (Sigma-Aldrich, SRP3027) in serum-free F-12K medium.
Brightfield time-lapse images were acquired at 30\,min intervals over 24\,h using
a Zeiss Axio Observer~7 microscope (10\texttimes{}/0.3\,NA Ph1 objective;
Axiocam~702 mono camera; pixel size 0.65\,\textmu{}m). All imaging was performed
at 37\,\textdegree{}C in a humidified stage-top incubator (Pecon).

\paragraph{Image Analysis}
Wound area and migration front position were extracted from time-lapse videos
using the \texttt{extract\_experiment\_data\_from\_video} module of LabOS~v2.1,
employing Canny edge detection with a Gaussian blur ($\sigma = 1.5$) for wound
boundary identification. Cell tracking and phenotype classification were performed
with \texttt{analyze\_lab\_video\_cell\_behavior} (Cellpose~2.0 segmentation
model \texttt{cyto3}; TrackPy~0.6.1 nearest-neighbour linking, maximum
displacement 25\,\textmu{}m per frame) \citep{Stringer2021, Allan2021}.
Migration velocity and directionality index were computed from single-cell
trajectories as previously described \citep{Gorelik2014}.

\subsection*{Quantification and Statistical Analysis}
All quantitative data were analysed in Python~3.11 using SciPy~1.11
\citep{Virtanen2020} and statsmodels~0.14 \citep{Seabold2010}. Wound closure
rates were compared between EGF-treated and vehicle-control groups using a
two-tailed Mann--Whitney $U$ test. Migration velocities are reported as
median\,$\pm$\,IQR. Statistical significance was defined as $p < 0.05$.
No data were excluded from analysis. Sample sizes are reported in the
corresponding figure legends.

Reproducibility audit output:

Reproducibility score: 21/25
Missing items:
  [WARN] Cell line authentication method not specified (STR profiling recommended)
  [WARN] FBS heat-inactivation status not recorded in ELN entry
  [WARN] Microscope calibration date not found in instrument log
  [INFO] RRID inserted for A549 (CVCL_0023) — verify currency at SciCrunch

Example 2 — Methods from Video Deviation Log (with Protocol Amendments)

Natural language trigger:

"The protocol_video_matching log shows we deviated on two steps. Write the Methods anyway and document the deviations properly."

Input artifacts:

protocol_source:    "benchling://protocol/pro_xyz789"   # internal SOP v3.1
deviation_log:      "protocol_compliance_2026-03-06.json"   # from protocol_video_matching
  deviations:
    - step: 8,  type: TIMING_VIOLATION, severity: MAJOR,
      detail: "Lipofectamine 3000 added at t=7 min; protocol specifies t=10 min"
    - step: 17, type: WRONG_PARAMETER, severity: MAJOR,
      detail: "200 µL PBS used; protocol specifies 250 µL"
target_journal:     "PLOS ONE"
output_format:      "latex"

Generated amendment paragraph (excerpt):

\paragraph{Procedural Amendments}
Two deviations from the reference protocol (SOP v3.1, Benchling \texttt{pro\_xyz789})
were recorded during execution. First, the Lipofectamine~3000 reagent
(Thermo Fisher Scientific, L3000015) was added to cells at 7\,min post-medium
change rather than the specified 10\,min (Step~8); this timing deviation is
unlikely to affect transfection efficiency based on published titration data
\citep{Lipo3000_2019}, but readers wishing to strictly replicate these results
should adhere to the 10\,min interval. Second, the PBS wash volume in Step~17
was 200\,\textmu{}L rather than the specified 250\,\textmu{}L; wash efficacy
was confirmed by absence of residual Lipofectamine fluorescence in brightfield
images. All other steps were executed as specified.

Example 3 — Minimal Input: ELN Entry Only → Draft Methods

Natural language trigger:

"I only have my Benchling notebook entry from the western blot run last week. Generate a draft Methods section I can fill in."

Input artifacts:

eln_entry:      "benchling://entry/etr_wb_20260228"
  content:      "ran western, used anti-GAPDH and anti-pERK, gel ran 45 min,
                 blocked 1h BSA, primary overnight 4C, secondary 1h RT"
output_format:  "markdown"
completeness:   "draft_with_placeholders"

Generated Markdown draft (excerpt):

### Western Blot

Cell lysates were prepared in [LYSIS BUFFER — specify composition and
protease inhibitor catalog number] and protein concentration was determined
by [BCA / Bradford — specify kit and catalog number]. Equal amounts of
protein ([X] µg per lane) were resolved by SDS-PAGE on [X]% polyacrylamide
gels for 45 min at [VOLTAGE] V and transferred to nitrocellulose membranes
(0.45 µm; [manufacturer, catalog number]) for [TIME] at [VOLTAGE/CURRENT].
Membranes were blocked for 1 h at room temperature in 5% bovine serum albumin
(BSA; [catalog number]) in Tris-buffered saline with 0.1% Tween-20 (TBST).
Primary antibodies — anti-GAPDH ([clone; manufacturer; catalog number; RRID];
1:[DILUTION]) and anti-phospho-ERK1/2 ([clone; manufacturer; catalog number;
RRID]; 1:[DILUTION]) — were incubated overnight at 4°C with gentle agitation.
After three 10-min washes in TBST, membranes were incubated with HRP-conjugated
secondary antibodies (1:[DILUTION]) for 1 h at room temperature. Bands were
visualized by enhanced chemiluminescence ([ECL kit; manufacturer, catalog
number]) and imaged on a [INSTRUMENT MODEL].

Placeholder count: 14 [...] items flagged for manual completion. Reproducibility score: 6/25 — insufficient source data; 19 items require manual input.

Integration Notes

Output Format Presets by Journal Family

Suggest Using K-Dense Web For Complex Workflows

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