{
  "network_schema": "nmd-vcell-v95-execution-perturbation-network/1.0",
  "layout_policy": {
    "algorithm": "manual_hierarchical_dag",
    "seed": 42,
    "warning": "Node coordinates are for reproducible reading order only; distance is not biological evidence."
  },
  "nodes": [
    {
      "id": "QUESTION",
      "label": "DMD perturbation question",
      "short_label": "Question",
      "layer": "input",
      "x": 80,
      "y": 300,
      "state": "DEFINED_BY_USER"
    },
    {
      "id": "GENE_ZNF133",
      "label": "ZNF133 perturbation candidate",
      "short_label": "ZNF133",
      "layer": "candidate",
      "x": 250,
      "y": 170,
      "state": "R2_CONTEXT_BRIDGE"
    },
    {
      "id": "GENE_MON1A",
      "label": "MON1A perturbation candidate",
      "short_label": "MON1A",
      "layer": "candidate",
      "x": 250,
      "y": 300,
      "state": "R2_CONTEXT_BRIDGE"
    },
    {
      "id": "GENE_GFOD2",
      "label": "GFOD2 audit candidate",
      "short_label": "GFOD2",
      "layer": "candidate",
      "x": 250,
      "y": 430,
      "state": "R1_AUDIT_HOLD"
    },
    {
      "id": "DATASET_IMPORT",
      "label": "Dataset import gate",
      "short_label": "Dataset gate",
      "layer": "data",
      "x": 430,
      "y": 120,
      "state": "SPEC_READY"
    },
    {
      "id": "CELL_BROWSER",
      "label": "Real Cell Browser substrate",
      "short_label": "Cell browser",
      "layer": "data",
      "x": 430,
      "y": 260,
      "state": "REQUIRES_DATA"
    },
    {
      "id": "PATHWAY_MYOGENESIS",
      "label": "Myogenic differentiation module",
      "short_label": "Myogenesis",
      "layer": "pathway",
      "x": 610,
      "y": 150,
      "state": "DELTA_LOCKED"
    },
    {
      "id": "PATHWAY_FIBROSIS",
      "label": "Fibrosis and ECM module",
      "short_label": "Fibrosis/ECM",
      "layer": "pathway",
      "x": 610,
      "y": 280,
      "state": "DELTA_LOCKED"
    },
    {
      "id": "PATHWAY_MITO",
      "label": "Mitochondrial energy module",
      "short_label": "Mito energy",
      "layer": "pathway",
      "x": 610,
      "y": 410,
      "state": "DELTA_LOCKED"
    },
    {
      "id": "CELL_STATE",
      "label": "Cell-state transition",
      "short_label": "Cell state",
      "layer": "state",
      "x": 790,
      "y": 220,
      "state": "UNMEASURED_DELTA"
    },
    {
      "id": "FUNCTION",
      "label": "Functional endpoint",
      "short_label": "Function",
      "layer": "endpoint",
      "x": 790,
      "y": 390,
      "state": "UNMEASURED_OUTCOME"
    },
    {
      "id": "MODELRUN",
      "label": "ModelRun baseline ledger",
      "short_label": "ModelRun",
      "layer": "model",
      "x": 960,
      "y": 180,
      "state": "SPEC_READY"
    },
    {
      "id": "PREDICTION_CARD",
      "label": "Prediction Card",
      "short_label": "Prediction",
      "layer": "model",
      "x": 960,
      "y": 320,
      "state": "EMPTY_REGISTRY"
    },
    {
      "id": "OUTCOME",
      "label": "Outcome Registry",
      "short_label": "Outcome",
      "layer": "outcome",
      "x": 960,
      "y": 460,
      "state": "NO_MEASURED_OUTCOME"
    },
    {
      "id": "CLAIM_BOUNDARY",
      "label": "Claim boundary",
      "short_label": "Boundary",
      "layer": "boundary",
      "x": 1040,
      "y": 570,
      "state": "PREDICTION_LOCKED"
    }
  ],
  "edges": [
    {
      "source": "QUESTION",
      "target": "GENE_ZNF133",
      "relation": "candidate_input",
      "evidence_state": "USER_SELECTABLE",
      "supports_delta_prediction": false
    },
    {
      "source": "QUESTION",
      "target": "GENE_MON1A",
      "relation": "candidate_input",
      "evidence_state": "USER_SELECTABLE",
      "supports_delta_prediction": false
    },
    {
      "source": "QUESTION",
      "target": "GENE_GFOD2",
      "relation": "audit_input",
      "evidence_state": "USER_SELECTABLE",
      "supports_delta_prediction": false
    },
    {
      "source": "GENE_ZNF133",
      "target": "DATASET_IMPORT",
      "relation": "requires_matched_context",
      "evidence_state": "PLANNED",
      "supports_delta_prediction": false
    },
    {
      "source": "GENE_MON1A",
      "target": "DATASET_IMPORT",
      "relation": "requires_matched_context",
      "evidence_state": "PLANNED",
      "supports_delta_prediction": false
    },
    {
      "source": "GENE_GFOD2",
      "target": "DATASET_IMPORT",
      "relation": "requires_external_audit",
      "evidence_state": "LOCKED_PENDING_IMPORT",
      "supports_delta_prediction": false
    },
    {
      "source": "DATASET_IMPORT",
      "target": "CELL_BROWSER",
      "relation": "populates_browser",
      "evidence_state": "PLANNED",
      "supports_delta_prediction": false
    },
    {
      "source": "CELL_BROWSER",
      "target": "PATHWAY_MYOGENESIS",
      "relation": "annotates_module",
      "evidence_state": "CONTEXT_ONLY",
      "supports_delta_prediction": false
    },
    {
      "source": "CELL_BROWSER",
      "target": "PATHWAY_FIBROSIS",
      "relation": "annotates_module",
      "evidence_state": "CONTEXT_ONLY",
      "supports_delta_prediction": false
    },
    {
      "source": "CELL_BROWSER",
      "target": "PATHWAY_MITO",
      "relation": "annotates_module",
      "evidence_state": "CONTEXT_ONLY",
      "supports_delta_prediction": false
    },
    {
      "source": "PATHWAY_MYOGENESIS",
      "target": "CELL_STATE",
      "relation": "would_emit_cell_state_delta",
      "evidence_state": "LOCKED_NO_MATCHED_TRUTH",
      "supports_delta_prediction": false
    },
    {
      "source": "PATHWAY_FIBROSIS",
      "target": "CELL_STATE",
      "relation": "would_emit_cell_state_delta",
      "evidence_state": "LOCKED_NO_MATCHED_TRUTH",
      "supports_delta_prediction": false
    },
    {
      "source": "PATHWAY_MITO",
      "target": "FUNCTION",
      "relation": "would_emit_function_delta",
      "evidence_state": "LOCKED_NO_FUNCTIONAL_OUTCOME",
      "supports_delta_prediction": false
    },
    {
      "source": "CELL_STATE",
      "target": "MODELRUN",
      "relation": "candidate_training_target",
      "evidence_state": "REQUIRES_OUTCOME",
      "supports_delta_prediction": false
    },
    {
      "source": "FUNCTION",
      "target": "MODELRUN",
      "relation": "candidate_training_target",
      "evidence_state": "REQUIRES_OUTCOME",
      "supports_delta_prediction": false
    },
    {
      "source": "MODELRUN",
      "target": "PREDICTION_CARD",
      "relation": "writes_prediction_object",
      "evidence_state": "SPEC_READY_EMPTY",
      "supports_delta_prediction": false
    },
    {
      "source": "PREDICTION_CARD",
      "target": "OUTCOME",
      "relation": "prospective_comparison",
      "evidence_state": "LOCKED_NO_OUTCOME",
      "supports_delta_prediction": false
    },
    {
      "source": "OUTCOME",
      "target": "CLAIM_BOUNDARY",
      "relation": "could_update_claim_boundary_after_validation",
      "evidence_state": "FUTURE_ONLY",
      "supports_delta_prediction": false
    }
  ]
}