{
  "version": 3,
  "created_at": "2026-07-09T14:29:36.755Z",
  "task_summary": "Write standalone EoE de novo binder-design manuscript with full supplemental figure set",
  "agents": [],
  "phases": [
    {
      "name": "Plan",
      "delegations": [
        {
          "steps": [
            {
              "title": "Inventory data artifacts and define figure plan",
              "description": "Pull every relevant artifact from the project store (eoe_meta_signature.csv, eoe_target_shortlist.csv, eoe_crossref_lit_vs_omics.csv, sc_celltype_de.csv, target_hotspots.json, backbone QC CSVs, mpnn_scored.csv 1920 seqs, eoe_binder_validation.csv 60 complexes, lead specs, existing PNGs/videos). Build a manifest mapping each planned main + supplemental figure to its data source. Derive the paper narrative arc with derive_paper_brief and a handling-editor review to fix main-vs-supplement figure assignment. Output: figure_plan.json."
            },
            {
              "title": "Generate target-selection supplemental figures",
              "description": "From meta-analysis + cross-reference + single-cell data, render publication-grade panels: (S1) volcano/forest of the 9-cohort meta-analysis highlighting CCL26/POSTN; (S2) lit-vs-omics concordance scatter (reuse/upgrade existing); (S3) single-cell cell-of-origin dotplot for CCL26/POSTN/CAPN14; (S4) omics druggability shortlist ranking bar. Use apply_figure_style() and render-then-verify overlap checks. Save each PNG."
            },
            {
              "title": "Generate design-pipeline supplemental figures",
              "description": "From backbones + MPNN data: (S5) RFdiffusion backbone QC — binder length, Rg, hotspot-contact distributions per target; (S6) epitope definition + SASA (reuse target_epitopes.png, upgrade if needed); (S7) SolubleMPNN score distributions across 1920 sequences by temperature and target; (S8) sequence-complexity filter effect (entropy/max-run/top-aa before vs after). Publication-grade, saved as PNGs."
            },
            {
              "title": "Generate validation supplemental figures",
              "description": "From eoe_binder_validation.csv (60 complexes): (S9) ipTM vs pLDDT scatter for all 60 with pass thresholds (upgrade foldback_metrics.png); (S10) epitope-coverage distribution per target; (S11) on-target score ranking of all 30/target; (S12) per-lead interface contact maps / buried-surface breakdown. Include a panel of the two lead complexes (still renders from PyMOL). Saved as PNGs."
            },
            {
              "title": "Compose main figures",
              "description": "Assemble 4-5 main figures from the strongest panels using figure-composer: Fig1 = graphical abstract/hook (two-target cascade schematic + lead complexes + headline metrics); Fig2 = target selection (meta-analysis + concordance + cell-of-origin); Fig3 = design pipeline schematic + backbone/sequence funnel; Fig4 = fold-back validation (ipTM/pLDDT + on-target + leads); Fig5 = lead binder structures with epitope engagement. Multi-panel, labeled, publication-grade."
            },
            {
              "title": "Draft manuscript text",
              "description": "Write full manuscript in markdown: Title, Abstract, Introduction (EoE unmet need, CCL26 chemokine axis, POSTN barrier persistence), Results (target selection, pipeline, validation, two leads), Methods (RFdiffusion params, SolubleMPNN, Boltz-2, on-target scoring, video render), Discussion (mechanism, limitations, wet-lab next steps), with in-text figure/table callouts and a references section grounded in the PMIDs already gathered. Honest in-silico caveats throughout."
            },
            {
              "title": "Assemble supplemental document and legends",
              "description": "Write supplemental_information.md collecting all supplemental figures with full legends, supplemental tables (validation CSV, MPNN summary, backbone QC, target shortlist) referenced as artifacts, and methods detail overflow. Cross-link main text callouts (Fig S1-S12, Table S1-Sn)."
            },
            {
              "title": "Compile to PDF and finalize",
              "description": "Render the main manuscript markdown to PDF (with embedded main figures) via pandoc or a matplotlib/HTML route available in-env. Verify all figures embed and resolve. Save manuscript PDF + markdown + all figures + supplemental doc as artifacts. Provide a final artifact index."
            }
          ]
        }
      ],
      "id": "phase-0"
    }
  ],
  "desired_outputs": [
    "Main manuscript (markdown + PDF) with abstract, intro, methods, results, discussion",
    "Main figure set (4-5 publication-grade figures)",
    "Supplemental figures (8-12) supporting target selection, design, and validation",
    "Supplemental tables (CSV-backed) and figure/table legends"
  ],
  "feasibility": {
    "rationale": "All underlying data exist as project artifacts (target selection, cross-reference, 80 backbones, 1920 MPNN sequences, 60 fold-back complexes, 2 leads, videos). The task is composition + figure generation, not new computation, so confidence is high. The main uncertainty is scope of the supplemental set, which we'll bias toward comprehensive.",
    "confidence": "high"
  }
}