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Scenario book: drafting manuscript results from accumulated evidence

Goal

Write a scenario showing a researcher who has accumulated enough evidence for hypothesis H2 (spindle topography) and now wants to draft the results section with publication-quality figures.

Context

This scenario exercises the evidence-to-manuscript workflow: questio-ready check → evidence collection → figure design with figio → manuscript section drafting with manuscripto. It's the payoff phase — where all the careful evidence recording finally produces a manuscript section.

The scenario should be written at docs/specs/research-orchestration/scenarios/scenario-manuscript-drafting.md.

Pixecog context: - H2: "What are the cortical origins of ripple-driving spindles?" — milestones: spindle-detection-validated, spindle-topography-mapped - Manuscript section: results/h2-spindle-origins - Existing manuscript structure at docs/manuscript/pixecog/ with intro, methods, placeholder results - Methods section (10.5 KB) describes 5 rats, ECoG 512 contacts, Neuropixels 212 contacts - Figures needed: spindle topography heatmaps, detection rate distributions, spatial maps - figio can produce FigureSpec YAML → panel rendering → SVG composition → PDF/PNG - manuscripto: manuscript_section_context, manuscript_assemble, manuscript_build, manuscript_cite_check - biblio: manuscript_cite_suggest for finding missing citations

Prompt

Write the scenario at /storage2/arash/projects/projio/docs/specs/research-orchestration/scenarios/scenario-manuscript-drafting.md.

Step 1: Read context. - Read /storage2/arash/projects/projio/docs/specs/research-orchestration/scenario-book.md for format - Read pixecog's manuscript structure if accessible - Read the figio design spec if it exists (check /storage2/arash/projects/projio/docs/specs/figio/)

Step 2: Write the scenario.

Structure: 1. Header with starting state: H2 milestones are complete, evidence is recorded, manuscript section is a placeholder 2. Phase 1: Readiness check — researcher says "H2 should have enough evidence now. Can we draft the results?" Agent calls questio_status("H2") — confirms both milestones complete with validated evidence. Calls questio_gap("H2") — no gaps. Uses the questio-ready skill pattern: "H2 has sufficient evidence, manuscript section results/h2-spindle-origins is draftable." 3. Phase 2: Evidence collection — Agent gathers all result notes for H2: note_search(tags=["result"], series="spectrogram_burst"). Retrieves 3-4 result notes with metrics, figures, and observations. Presents a structured evidence summary to the researcher. 4. Phase 3: Figure design — Researcher says "I need a figure showing the spindle topography across the cortical surface." Agent uses figio_figure_list to check existing specs, then proposes a FigureSpec YAML for a multi-panel figure: (A) mean spindle rate per contact, (B) spindle amplitude heatmap, (C) example waveforms from key regions. Uses figio_edit_spec and figio_build to create the figure. Iterate on layout based on human feedback. 5. Phase 4: Section drafting — Agent uses manuscript_section_context("results/h2-spindle-origins") to get the template and surrounding context. Drafts the results section, weaving evidence from result notes into scientific prose. Uses manuscript_cite_check to verify all claims have citations, manuscript_cite_suggest for any gaps. 6. Phase 5: Build and review — manuscript_assemble to compile the full manuscript, manuscript_build to render PDF. Researcher reviews, gives feedback on prose ("too much detail on methods here, that belongs in the Methods section"). Agent iterates. 7. Phase 6: Polish — manuscript_journal_check to verify formatting against target journal requirements. Final commit.

Use mkdocs material admonitions: - !!! info "Behind the scenes" for tool calls - !!! tip "Evidence trail" for showing how result notes feed into prose - !!! example "Generated figure" for figio output descriptions - !!! warning "Human checkpoint" for prose quality review - !!! note "Citation management" for biblio/cite_check details

End with: ecosystem coverage (questio + figio + manuscripto + biblio — the full publication pipeline), loop patterns, key insight (answer: the manuscript writes itself when evidence is properly structured — questio-record's structured frontmatter directly feeds manuscript drafting).

Step 3: Commit with message: "Add scenario: drafting manuscript results from accumulated evidence"

Acceptance Criteria

  • [ ] File at docs/specs/research-orchestration/scenarios/scenario-manuscript-drafting.md
  • [ ] Exercises questio (readiness), figio (figures), manuscripto (drafting/building), biblio (citations)
  • [ ] Shows the evidence → figure → prose → build pipeline
  • [ ] Iterate loop for figure design and prose refinement
  • [ ] Uses mkdocs material admonitions
  • [ ] Committed

Batch Result

  • status: done
  • batch queue_id: 140acc720c2b
  • session: 49cfe4a4-561d-4bb8-8fb6-d01b2ac17020
  • batch duration: 801.3s