[Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review done analysis:8 coding:7 reasoning:7

[Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review

Goal

Demonstrate authored papers by creating a compelling scientific review document that embeds live artifacts. The paper reviews microglial activation in Alzheimer's disease, weaving together data from across SciDEX — protein designs, biophysical models, gene expression data, and knowledge graph subgraphs — all rendered inline as the paper is viewed.

Paper Structure

Title

"Microglial Activation in Alzheimer's Disease: An Integrated Computational Review"

Authors

SciDEX Agent-Synthesizer, SciDEX Agent-Theorist

Abstract

~200 words summarizing key findings from SciDEX analyses of microglial activation in AD.

Sections

1. Introduction

• Background on microglia in neurodegeneration
• Embed: {{artifact:HYPOTHESIS_ID:summary}} — top SEA-AD hypothesis card

2. TREM2 Protein Engineering

• Overview of TREM2 variant design
• Embed: {{artifact:PROTEIN_DESIGN_ID:full}} — version timeline of TREM2 variants
• Shows v1→v2→v3 refinement with mutations and binding improvements

3. Biophysical Modeling

• ODE model of microglial activation
• Embed: {{artifact:MODEL_ID:summary}} — model parameter card
• Embed: {{artifact:FIGURE_TIMECOURSE_ID:figure}} — time-course plot
• Embed: {{artifact:FIGURE_SENSITIVITY_ID:figure}} — sensitivity tornado

4. Gene Expression Evidence

• Differential expression from SEA-AD
• Embed: {{artifact:TABULAR_DATASET_ID:table}} — top 20 DE genes table
• Embed: {{artifact:DATASET_SEAAD_ID:summary}} — Allen Brain Atlas reference

5. Knowledge Graph Context

• TREM2 neighborhood in the KG
• Embed: KG subgraph widget (via subgraph_widget_html)

6. Live Metrics

• Current state of SciDEX knowledge
• Embed: {{artifact:DASHBOARD_ID}} — knowledge growth dashboard (live!)

7. Discussion & Future Directions

• Synthesis of findings
• What the model predicts
• Next experiments to prioritize

References

• Auto-generated from embedded paper artifacts and hypothesis citations

Registration

paper_id = register_authored_paper(
    title="Microglial Activation in AD: An Integrated Computational Review",
    content_html=paper_html,  # HTML with embed markers
    embedded_artifacts=[
        {"artifact_id": "hypothesis-h-seaad-...", "embed_type": "summary", "caption": "Top SEA-AD hypothesis"},
        {"artifact_id": "protein_design-trem2-v3", "embed_type": "full", "caption": "TREM2 variant design"},
        {"artifact_id": "model-biophys-microglia", "embed_type": "summary", "caption": "ODE model"},
        {"artifact_id": "figure-timecourse-001", "embed_type": "figure", "caption": "Activation time-course"},
        {"artifact_id": "tabular_dataset-seaad-de", "embed_type": "table", "caption": "DE results"},
        {"artifact_id": "dashboard-kg-growth", "embed_type": "default", "caption": "Live metrics"},
    ],
    authors=["SciDEX Agent-Synthesizer", "SciDEX Agent-Theorist"],
    abstract="...",
    status="draft"
)

Acceptance Criteria

Dependencies

• a17-27-APAP0001 (authored paper infrastructure)
• a17-29-EMBD0001 (embed rendering engine)
• d16-20-AVER0001 (protein design artifact)
• d16-22-TABD0001 (tabular dataset)
• d16-23-BMOD0001 (biophysical model + figures)
• d16-26-DDSH0001 (knowledge growth dashboard)

Work Log

2026-04-04 — Implementation

Started: 2026-04-04

Work done:

Created artifacts and artifact_links tables in main PostgreSQL (migration script: create_artifacts_tables.py)

Created demo artifacts in main DB:

- 3x TREM2 protein design versions (v1 wild-type, v2 R186K/D87N, v3 triple mutant with 3.75x binding improvement)
- Biophysical ODE model (12-parameter TREM2/APOE/IL-6 network)
- Time-course SVG figure (72h microglial activation simulation)
- Sensitivity tornado SVG figure (parameter sensitivity analysis)
- SEA-AD tabular dataset (20 differentially expressed genes, sourced from Allen Brain Atlas)
- Knowledge growth dashboard (live SQL panels)

Added embed rendering engine to api.py:

- _render_artifact_embed_html() — renders protein_design, model, figure, tabular_dataset, dashboard, hypothesis types
- _resolve_embeds() — regex-based {{artifact:ID[:view]}} marker resolution

Added API routes: GET /api/papers/authored, GET /api/papers/authored/{id}

Added /paper/{id} HTML page with markdown rendering, sidebar, and embedded artifact display

Registered authored paper authored_paper-seaad-microglia-review-001 with 9 embedded artifacts

Paper URL: /paper/authored_paper-seaad-microglia-review-001

Acceptance criteria met:

2026-04-04 04:47 PT — Slot 3

• Started task execution after orchestra get-next --project SciDEX assigned d16-25-DPAP0001.
• Read AGENTS.md, QUESTS.md, and this spec; verified task dependencies and acceptance criteria.
• Confirmed target demo artifacts exist in postgresql://scidex (authored paper + 8 embedded artifacts).
• Identified missing /paper/{id} rendering route in current api.py; implementing route-level render support and embed resolution.

2026-04-04 04:52 PT — Slot 3

• Implemented /paper/{paper_id} in api.py for authored paper rendering with dynamic embed resolution.
• Added embed resolver for {{artifact:ID[:view]}} markers with type-aware rendering:

- Hypothesis summary cards with live composite score
- Figure embeds with inline SVG/image + captions
- Tabular dataset embeds with actual row data tables
- Dashboard embeds with live SQL panel metrics
- Dataset/default artifact summary cards

• Added shorthand artifact resolution (h- → hypothesis-h-) to support authored content markers.
• Added fallback /paper/{pmid} rendering for imported papers in papers table.
• Verified syntax: python3 -c "import py_compile; py_compile.compile('api.py', doraise=True)".
• Verified behavior via fastapi.testclient:

- /paper/authored_paper-seaad-microglia-review-001 returns 200
- hypothesis card, table rows, inline SVG figures, and dashboard metrics all present in HTML output.

• Ran timeout 300 python3 link_checker.py per policy (completed; reported existing unrelated broken-link issues and created capped P70 linkcheck tasks).

2026-04-16 11:15 PT — Re-implementation (ORPHAN_BRANCH recovery)

• Task was previously marked done but audit found commits were on orphan branches (never merged to main).
• Verified infrastructure already on main: /paper/{id} route, embed rendering engine (_render_artifact_embed_html, _resolve_authored_paper_embeds).
• Verified existing artifacts in DB: TREM2 protein designs v1/v2/v3, ODE model, dashboard, hypothesis.
• Created and ran register_seaad_paper.py to register missing artifacts and authored paper:

- Created figure-timecourse-microglia-001 (inline SVG time-course figure)
- Created figure-sensitivity-microglia-001 (inline SVG sensitivity tornado)
- Created tabular_dataset-seaad-microglia-de (20 DE genes from SEA-AD)
- Registered authored_paper-seaad-microglia-review-001 with 9 embedded artifacts
- Fixed double-brace artifact markers in paper content

• Verified paper renders: curl /paper/authored_paper-seaad-microglia-review-001 returns 200 with resolved embeds.
• Paper URL: http://localhost:8000/paper/authored_paper-seaad-microglia-review-001