{
  "version": 3,
  "created_at": "2026-07-11T21:04:11.977Z",
  "task_summary": "Turn the EAC dual-arm drug program into a bioRxiv preprint with two peer-review rounds and four deliverables",
  "agents": [],
  "phases": [
    {
      "name": "Plan",
      "delegations": [
        {
          "steps": [
            {
              "title": "Lock figure story and manuscript outline",
              "description": "Load paper-narrative and derive the figure-driven arc from the dossier abstract + existing figure captions. Decide the 4-figure set: Fig 1 = EAC genomics + competitive whitespace + trajectory-spanning two-arm strategy schematic (the hook); Fig 2 = target triage/nomination with honest druggability filter; Fig 3 = de novo binder design pipeline + in-silico validation results; Fig 4 = rendered lead complex structures (gucy2c_bb2, dkk1_bb1) with interface annotation. Produce a written outline (sections, per-figure claims, supplement list) saved as manuscript_outline.md."
            },
            {
              "title": "Compose the manuscript figures",
              "description": "Load figure-composer/figure-style. Reuse the three existing publication-grade panels (eac_driver_landscape, eac_whitespace_map, design_results) where they stand, and compose the new panels: a trajectory/strategy schematic for Fig 1 and rendered 3D complex structures for Fig 4 (render gucy2c_bb2_complex.pdb and dkk1_bb1_complex.pdb, binder vs target chains colored, epitope patch highlighted). Deliver figure1.png–figure4.png plus a supplementary figure if needed."
            },
            {
              "title": "Draft the full manuscript text",
              "description": "Write a bioRxiv-style preprint: Title, Abstract, Introduction (EAC unmet need + novelty-first rationale), Results (genomics/whitespace → target nomination → dual-arm selection → de novo design → in-silico validation), Methods (data sources, target-structure prep, RFdiffusion→ProteinMPNN→Boltz-2 parameters, triage logic), Discussion (strengths, the two make-or-break open questions O-2/O-4, limitations), and a data/code availability + author-contribution stub. Every quantitative claim tied to an upstream artifact. In-silico and projection claims explicitly flagged. Save as manuscript.md."
            },
            {
              "title": "Verify key external claims against real sources",
              "description": "Use literature-review to confirm the factual anchors that are NOT internal computation: the approved-EAC-drug precedents (trastuzumab, pembro/nivo incl. adjuvant, ramucirumab, T-DXd, zolbetuximab 2024), DKN-01/DKK1 clinical precedent, EAC epidemiology (~22,370 US cases, rising incidence), and Barrett's prevalence. Replace any unverifiable citation; never fabricate. Produce a references.md with resolved DOIs/PMIDs and a claims-to-source trace table."
            },
            {
              "title": "Assemble supplemental files",
              "description": "Bundle supplements: S1 all 16 binder designs (from design_leads.csv with sequences/ipTM/pLDDT), S2 target nomination table, S3 competitive landscape table, S4 detailed computational methods + parameters, S5 epitope/cross-reactivity note, and the go/no-go gate table (G1–G5) + open questions (O-1–O-5). Save as a supplementary_information.md plus the supporting CSVs, and a manuscript_v1 bundle."
            },
            {
              "title": "Peer-review round 1",
              "description": "Run synthetic-peer-review on manuscript_v1 with 3 complementary expert personas (computational protein design; GI/thoracic oncology + translational; regulatory/clinical-development), each briefed on the correct framing (AI-generated, in-silico, wet-lab explicitly out of scope). Capture 3 reviews + a handling-editor decision letter with a prioritized Essential-Revisions list. Save peer_review_round1.md."
            },
            {
              "title": "Revise to v2 and run peer-review round 2",
              "description": "Incorporate round-1 Essential Revisions into manuscript_v2, tracking every change in a revision log (reviewer point → response → what changed). Re-run synthetic-peer-review on v2 for a second round; capture the second decision letter and any residual points. Save manuscript_v2.md, revision_log.md, and peer_review_round2.md."
            },
            {
              "title": "Produce the four bundled deliverables",
              "description": "Assemble the exact four deliverables the profile ships: (1) executive_summary.md — one-page summary of the paper and its impact; (2) the final manuscript + supplemental files (manuscript_final.md + supplementary_information.md + figures); (3) peer_review_report.md — editor/reviewer comments across BOTH rounds plus the revisions made in response; (4) lay_abstract.md — plain-language abstract for non-specialists. Save all as artifacts and present the bundle with links."
            }
          ]
        }
      ],
      "id": "phase-0"
    }
  ],
  "feasibility": {
    "rationale": "All upstream artifacts are present and internally consistent (10-stage dossier, three strategy briefs, validated in-silico design leads, three publication-grade figures, two complex structures). The task is communication of completed work, not new science. Main care point: keeping every claim traceable and honestly flagging in-silico/unvalidated results — which the source material already does.",
    "confidence": "high"
  }
}