{ "execution_schema": "nmd-vcell-v95-execution-layer/1.0", "resource_release": "v1.0.0-database-resource", "evidence_freeze": "2026-07-25", "interface_build": "EA-20260730-42", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "generated_date": "2026-08-01", "derived_from": { "blueprint": "api/v1.1/competitive_upgrade_blueprint.json", "blueprint_schema": "nmd-vcell-competitive-upgrade-blueprint/1.0", "blueprint_lesson_count": 6 }, "headline": "V95 converts the V94 competitive benchmark blueprint into executable release objects, network contracts and acceptance gates.", "execution_units": [ { "unit_id": "V95-DATASET-IMPORT", "axis": "Dataset import", "current_state": "EXECUTABLE_SPEC_READY", "next_action": "Register candidate DMD single-cell, single-nucleus and spatial datasets with donor, disease, state, perturbation and checksum fields before browsing.", "acceptance_gate": "At least two disease-relevant datasets have stable accessions, donor-level metadata, raw/processed SHA-256, license and prohibited-use fields.", "evidence_objects": [ "api/v1.1/dataset_registry.json", "api/v1.1/competitive_upgrade_blueprint.json" ], "unlocks": "Real Cell Browser v1 import queue; no prediction claim." }, { "unit_id": "V95-CELL-BROWSER", "axis": "Real Cell Browser", "current_state": "PLANNED_REQUIRES_DATA_IMPORT", "next_action": "Replace concept-only context cards with donor-filtered cell-state panels, expression lookup, pseudobulk differential tables and exportable selections.", "acceptance_gate": "Browser selections resolve to Dataset object IDs and never summarize disease effect without donor-aware aggregation.", "evidence_objects": [ "/resource/cell-browser/", "api/v1.1/dataset_registry.json" ], "unlocks": "Inspectable cell-state substrate for future perturbation interpretation." }, { "unit_id": "V95-MODELRUN", "axis": "ModelRun adapter", "current_state": "EXECUTABLE_SPEC_READY", "next_action": "Run zero, train-mean, nearest-neighbour and ridge baselines under a shared immutable ModelRun envelope before any new model is promoted.", "acceptance_gate": "Each run records model id, commit, container digest, data release, split id, seed, metrics, logs and failure reason.", "evidence_objects": [ "api/v1.1/model_registry.json", "api/v1.1/benchmark_suite.json" ], "unlocks": "Comparable baseline ledger; calibrated DMD model count remains zero." }, { "unit_id": "V95-PERTURBATION-NETWORK", "axis": "Perturbation delta network", "current_state": "CONTRACT_READY_DELTA_LOCKED", "next_action": "Bind candidate perturbations to pathway modules, cell-state transitions, functional readouts and the missing evidence edge that would unlock each delta.", "acceptance_gate": "Every edge declares observed, inferred, planned or locked state; layout seed is fixed and node position is not interpreted as biology.", "evidence_objects": [ "api/v1.1/v95_execution_network.json", "api/v1.1/perturbation_cascade_network.json" ], "unlocks": "Network-shaped experiment design, not a pathway-delta prediction." }, { "unit_id": "V95-PROSPECTIVE-BENCHMARK", "axis": "Prospective benchmark", "current_state": "SPEC_READY_NO_HIDDEN_OUTCOMES", "next_action": "Freeze Study Card, Prediction Card and Outcome slots before laboratory outcomes are visible.", "acceptance_gate": "Timestamped prediction objects exist before outcome access, with null, toxic, failed-QC and abstained outcomes preserved.", "evidence_objects": [ "api/v1.1/study_card_manifest.json", "api/v1.1/prediction_registry.json" ], "unlocks": "Future hidden-test discipline; no current P1/P2 unlock." }, { "unit_id": "V95-OUTCOME-CHAIN", "axis": "Outcome return path", "current_state": "OBJECT_SCHEMA_READY_NO_MEASURED_OUTCOME", "next_action": "Append measured outcomes to the same object chain that generated the study and prediction records.", "acceptance_gate": "Study -> Prediction -> Experiment -> Outcome IDs remain linked without regenerating downstream IDs from URL parameters.", "evidence_objects": [ "/resource/workbench", "api/v1.1/prediction_registry.json" ], "unlocks": "Prospective evidence accumulation once real outcomes arrive." } ], "execution_network": { "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 } ] }, "counts": { "execution_units": 6, "network_nodes": 15, "network_edges": 18, "runnable_specs_ready": 3, "emitted_dmd_pathway_delta_predictions": 0, "emitted_dmd_cell_state_delta_predictions": 0, "measured_independent_dmd_outcomes": 0 }, "hard_boundaries": [ "No DMD pathway delta is emitted in V95.", "No cell-state delta, functional effect probability or therapeutic rank is emitted in V95.", "Network layout is reproducible but not biological distance.", "A future claim change requires a timestamped Prediction Card before outcome access." ], "acceptance_tests": [ "Execution layer page links JSON, network JSON and TSV outputs.", "Every execution unit has a current state, next action and acceptance gate.", "Every network edge states evidence_state and supports_delta_prediction=false.", "Route QA includes the V95 execution layer.", "Health, manifest, Downloads checksum and route smoke remain PASS." ], "claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release." }