Skip to content

Scenario book: reproduce Siapas & Wilson 1998 coupling results

Goal

Write a scenario showing a researcher using projio to plan and execute reproduction of results from a classic paper (Siapas & Wilson 1998 — hippocampal-cortical spindle-ripple coupling) in their own dataset.

Context

This scenario exercises the biblio-heavy planning workflow: the researcher starts from a paper, extracts the key claims and methods, maps them to their own hypotheses and pipelines, identifies gaps, and executes. It demonstrates how biblio, questio, codio, and pipeio compose for literature-driven research.

The scenario should be written at docs/specs/research-orchestration/scenarios/scenario-reproduce-paper.md.

Pixecog context (use this for realistic details): - The paper @siapas_1998 is cited in H2 ("What are the cortical origins of ripple-driving spindles?") in plan/questions.yml - H2 milestones: spindle-detection-validated, spindle-topography-mapped - Relevant flows: spectrogram_burst (spindle detection), sharpwaveripple (ripple detection), coupling_spindle_ripple - cogpy has: SpindleDetector, RippleDetector, cross-correlogram tools - The paper's key finding: temporal correlation between hippocampal ripples and cortical spindles, suggesting a hippocampo-cortical dialogue during sleep - Pixecog has ECoG (512 contacts) + Neuropixels (212 contacts) simultaneous recordings — richer than the original paper's single-tetrode + EEG setup - bib/srcbib/ contains the citation; PDFs may or may not be fetched

Prompt

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

Step 1: Read for context and format. - Read the existing scenario book: /storage2/arash/projects/projio/docs/specs/research-orchestration/scenario-book.md — follow the same conversation format (Human:/Agent: blocks with tool calls shown behind the scenes) - Read the loop mechanisms spec: /storage2/arash/projects/projio/docs/specs/research-orchestration/loop-mechanisms.md - Read pixecog's questions.yml: /storage2/arash/projects/pixecog/plan/questions.yml — for H2 details - Read pixecog's milestones.yml: /storage2/arash/projects/pixecog/plan/milestones.yml

Step 2: Write the scenario.

Structure: 1. Header with title, metadata, starting state, what the researcher wants 2. Phase 1: Paper deep dive — researcher says "I want to reproduce Siapas & Wilson 1998 results in our data." Agent uses paper_context("@siapas_1998"), biblio_enrich, potentially biblio_pdf_fetch if PDF is missing, then biblio_docling to extract methods details. Agent synthesizes: key claims, methods used, expected values, what's reproducible with pixecog's setup. 3. Phase 2: Map to hypotheses — Agent calls questio_status, identifies H2 maps to this paper. Checks questio_gap("H2") — what milestones are needed. Shows the researcher how the paper's claims map to their hypothesis structure. 4. Phase 3: Audit existing capabilities — Agent calls codio_discover("spindle detection"), codio_get("cogpy"), pipeio_flow_status("spectrogram_burst"), pipeio_flow_status("coupling_spindle_ripple"). Reports: what code exists, what flows are configured, what's missing. 5. Phase 4: Identify gaps and plan — Agent synthesizes: "The paper uses cross-correlogram analysis. cogpy has cross_correlogram tools. But the coupling_spindle_ripple flow expects spindle detection output that doesn't exist yet (spindle-detection-validated is not_started). We need to run spectrogram_burst first." Creates an execution plan. 6. Phase 5: Execute first step — Enter iterate loop for spindle detection. Run for one subject, assess, human gives feedback. Show 1-2 iterations. 7. Phase 6: Record and plan forward — Record observation notes, show what the next session would tackle.

Use mkdocs material admonitions throughout: - !!! info "Behind the scenes" — for tool calls - !!! tip "Why this matters" — for explaining design decisions - !!! warning "Human checkpoint" — for moments requiring human judgment - !!! example "What the agent sees" — for tool output summaries - !!! note — for general explanations

Include at the end: - Ecosystem coverage table showing which projio subsystems were used - Loop patterns used in the scenario - Key insight — what this scenario demonstrates that others don't (answer: literature-first planning, where the paper drives the agenda)

Step 3: Ensure the file has proper mkdocs frontmatter if needed (or just a markdown title).

Step 4: Commit with message: "Add scenario: reproduce Siapas & Wilson 1998 coupling results"

Acceptance Criteria

  • [ ] File at docs/specs/research-orchestration/scenarios/scenario-reproduce-paper.md
  • [ ] Realistic conversation format matching scenario-book.md style
  • [ ] Uses actual pixecog details (citekeys, flow names, cogpy modules, milestone names)
  • [ ] Exercises biblio, questio, codio, pipeio in a natural flow
  • [ ] Uses mkdocs material admonitions
  • [ ] Shows both orient and iterate loop patterns
  • [ ] Committed

Batch Result

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