{ "manifest_schema": "nmd-vcell-release-manifest/1.1", "object_id": "RELEASE:v1.2.0-measured-dmd-evidence:EA-20260817-57", "release_role": "current_platform_release", "release_label": "Current platform release manifest", "release_display_label": "Measured DMD context \u00b7 0/21 candidate perturbation outcomes", "release_status": "CURRENT_PLATFORM_RELEASE_DMD_PREDICTION_LOCKED", "authoritative_manifest": "/resource/api/current/release_manifest.json", "compatibility_aliases": [ "/resource/api/v1/release_manifest.json", "/resource/api/v1.1/release_manifest.json" ], "base_publication_snapshot_manifest": "/resource/api/releases/v1.0.0-database-resource/release_manifest.json", "overlay_history": [ { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260806_stage5_93.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.93:20260806", "role": "superseded_research_workbench_overlay_archive", "sha256": "098426c963190608dd12120c0236cf874ef635d77f5fa73a3d730738e75b5415", "size_bytes": 23475257, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.94:20260806" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260806_stage5_94.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.94:20260806", "role": "superseded_research_workbench_overlay_archive", "sha256": "0e2a190fea12a6378e3d58bf41176ba0e18093f1773d66e04658bf25c3739814", "size_bytes": 23482598, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.95:20260806" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260806_stage5_95.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.95:20260806", "role": "superseded_research_workbench_overlay_archive", "sha256": "e952d8352bc4ecea65bdebfbc4af43f6d16b5a90017be3d61c3a39cac68775c6", "size_bytes": 23482569, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.96:20260806" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260806_stage5_96.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.96:20260806", "role": "superseded_research_workbench_overlay_archive", "sha256": "2dc337cf87576dfc084adc5be6311d5209d0be4acc3c520da6f64a0a94f141b6", "size_bytes": 6674365, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.97:20260903" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260903_stage5_97.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.97:20260903", "role": "superseded_research_workbench_overlay_archive", "sha256": "a0645d1c43a95f7cd8ee9c3a22475907fa7b4aaa6c0ba428f0f6eced738134dc", "size_bytes": 6722630, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.98:20260903" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260903_stage5_98.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.98:20260903", "role": "superseded_research_workbench_overlay_archive", "sha256": "e444b0c49ccf938362968410a8760fb64b14b73068df1319001564b9598b26c9", "size_bytes": 6722879, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.99:20260903" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260903_stage5_99.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.99:20260903", "role": "superseded_research_workbench_overlay_archive", "sha256": "24717ebf8cd76ae102ca50ab56906d8322aaad6a557760e5ad6f2369943945f0", "size_bytes": 6722878, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.100:20260903" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260903_stage5_100.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.100:20260903", "role": "superseded_research_workbench_overlay_archive", "sha256": "4051d88fd0d2524420e8e5cd7c643e0fb4ccc33778fa90fb1c1db41bc618e39e", "size_bytes": 6722879, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.101:20260904" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_101.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.101:20260904", "role": "superseded_research_workbench_overlay_archive", "sha256": "37a64ee377935598949cff8e3e4a19b209a85107e703913f67633d9936c453f8", "size_bytes": 6729201, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.102:20260904" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_102.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.102:20260904", "role": "superseded_research_workbench_overlay_archive", "sha256": "86b9d1f5db8c42e9f9542f993a298f9cd90ff028fc0ba4c5116b905b6c2724b4", "size_bytes": 6729196, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.103:20260904" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_103.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.103:20260904", "role": "superseded_research_workbench_overlay_archive", "sha256": "4cc67c082605bdb3de0342051e8279f95a278342a2e4fdf61ce05f23ed815aec", "size_bytes": 6728684, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.104:20260904" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_104.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.104:20260904", "role": "superseded_research_workbench_overlay_archive", "sha256": "d502e8e474e0338cce74b9a8e53a8ec6f34a186b302a47505019c27c16db3f90", "size_bytes": 6729776, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.105:20260904" }, { "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_105.tar.gz", "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.105:20260904", "role": "superseded_research_workbench_overlay_archive", "sha256": "d031876b41d75f766c430b474226d9932ed33f944b92d87eac18965900294af9", "size_bytes": 6733482, "superseded_by": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.106:20260904" } ], "resource": "NMD-VCell", "release_config": "config/release_manifest.json", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "gene_schema_version": "1.1", "research_object_schema_version": "1.3", "interface_label": "NMD-VCell Evidence & Experiment Workbench", "interface_build": "EA-20260817-57", "model_release": "ridge-safe-v2.3", "benchmark_protocol": "repeated-fold-v2.2", "prior_algorithm_version": "dmd-prior-qweighted-context-v0.9", "object_counts": { "comparison_released": 5, "decision_card_draft": 3, "detailed_audit_gene_released": 123, "external_authorization_dossier_released": 1, "gene_released": 17921, "model_run_frozen": 6, "measured_dmd_evidence_released": 1, "external_dmd_pathway_validation_released": 1, "protocol_panel_draft": 1, "prediction_readiness_released": 1, "prediction_registry_released": 1, "perturbation_network_released": 1, "prospective_holdout_role_sealed": 6, "release_released": 1, "scientific_program_released": 1, "no_wet_lab_evaluation_released": 1, "unipert_feasibility_released": 1, "study_card_draft": 21, "v1_release_gate_released": 1, "project_state_released": 1, "stage_a_panel_slot_assigned": 24, "stage_a_panel_slot_frozen": 0, "stage_a_candidate_gene_assigned": 14, "stage_a_calibration_control_assigned": 10, "registered_study": 0, "experiment_running": 0, "prediction_registered": 0, "outcome_measured": 0 }, "project_state": { "object_id": "PROJECTSTATE:v1.2.0-measured-dmd-evidence:DMD-MIN-PERTURBOME:1.1", "program_id": "DMD-MIN-PERTURBOME", "lifecycle_state": "PANEL_DRAFT_ASSIGNED_SIGNOFF_PENDING", "effective_at": "2026-08-06", "source_object": "config/project_state.json", "source_sha256": "441d52287efd78935e2d72f547b7ca503ad4d34c4167a052c1f6135a4f9b4d73", "public_object": "api/v1.4/project-state/DMD-MIN-PERTURBOME.json", "supersedes": "PROJECTSTATE:v1.0.0-database-resource:DMD-MIN-PERTURBOME:1.0", "base_release_parent": { "resource_release": "v1.0.0-database-resource", "object_id": "PROJECTSTATE:v1.0.0-database-resource:DMD-MIN-PERTURBOME:1.0", "public_object": "api/v1.4/project-state/releases/v1.0.0-database-resource/DMD-MIN-PERTURBOME.json" }, "current_release_context": { "resource_release": "v1.2.0-measured-dmd-evidence", "interface_build": "EA-20260817-57", "analysis_stages": [ "Stage C1 candidate pathway cascade", "Stage C2 measured DMD context" ], "disease_modules": [ "DMD", "FSHD", "DM1", "SMA" ], "candidate_dmd_response_outcomes": "0/21", "candidate_ranking_generated": false } }, "current_release_context": { "analysis_stages": [ "Stage C1 candidate pathway cascade", "Stage C2 measured DMD context" ], "disease_modules": [ "DMD", "FSHD", "DM1", "SMA" ], "multidisease_manifest": "/resource/api/v2/diseases/manifest.json", "candidate_dmd_response_outcomes": "0/21", "candidate_dmd_response_truth": "0/21", "candidate_level_dmd_pathway_predictions": 0, "prediction_status": "LOCKED", "doi": "DOI_PENDING" }, "version_axes": { "resource_release": "v1.2.0-measured-dmd-evidence", "base_publication_release": "v1.0.0-database-resource", "evidence_freeze": "2026-08-03", "schema_version": "1.1", "model_release": "ridge-safe-v2.3", "benchmark_release": "repeated-fold-v2.2", "interface_label": "NMD-VCell Evidence & Experiment Workbench", "interface_build": "EA-20260817-57", "formal_v1_candidate_label": "v1.0.0-database-resource", "canonical_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256" }, "canonical_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "database_v1_publication_snapshot": { "snapshot_schema": "nmd-vcell-database-v1-publication-snapshot/1.0", "resource_release": "v1.0.0-database-resource", "interface_build": "EA-20260802-46", "evidence_freeze": "2026-07-25", "source_commit": "d93c7c0bcff34673eac5a0f9f9ca127fc1c9a801", "status": "immutable_author_review_candidate_external_gates_pending", "canonical_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "overlay": { "filename": "nmd_vcell_research_workbench_overlay_v1.0.0_database_resource_20260802_stage5_88.tar.gz", "object_id": "FILE:OVERLAY:v1.0.0-database-resource:stage5.88:20260802", "role": "research_workbench_overlay_archive", "size_bytes": 3178743, "sha256": "04c982d002b3ab0ad44319d6327116086da3a87a182430e4d475a1e2ad60b2e1" }, "portable_ro_crate": { "filename": "nmd-vcell-v1.0.0-ro-crate.zip", "size_bytes": 24512546, "sha256": "17610896790b76d715300a1edbe1d6ee5cb573bceb9691d1b031136c7f40e9e8" }, "landing_path": "releases/v1.0.0-database-resource/", "manifest_path": "api/v1.1/releases/v1.0.0-database-resource.json", "claim_boundary": "This frozen database-paper snapshot contains the Stage B0 observed healthy-myoblast network. It contains no candidate-level DMD perturbation outcome, no validated DMD pathway prediction and no therapeutic claim." }, "canonical_archive": { "object_id": "BUNDLE:DATABASE_V1:STAGE5_44", "filename": "canonical_database_v1_release_bundle", "size_bytes": 49295320, "sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "role": "composite_database_v1_release_bundle", "coverage": "Composite formal database-v1 object identity candidate; release_layers retain individual file hashes." }, "analysis_core_archive": { "object_id": "FILE:CORE:v0.8.1:v24r1:20260722", "filename": "nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz", "size_bytes": 9677910, "sha256": "b88a3b9f1ae44b48d6ea3c2a568626229cc93f94d539b8ea30f55534aae41f36", "role": "analysis_core_archive", "layer_release": "v0.8.1-v24r1-20260722", "coverage": "Frozen analysis core predating the Evidence Atlas interface; not a complete archive of the current public overlay." }, "release_layers": [ { "layer": "analysis_core", "required_for_composite_release": true, "archive": { "object_id": "FILE:CORE:v0.8.1:v24r1:20260722", "filename": "nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz", "size_bytes": 9677910, "sha256": "b88a3b9f1ae44b48d6ea3c2a568626229cc93f94d539b8ea30f55534aae41f36" } }, { "layer": "evidence_atlas_overlay", "required_for_composite_release": true, "archive": { "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.106:20260904", "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_106.tar.gz", "size_bytes": 7206687, "sha256": "3733a936e8ba0d0da7336e3d5631b1b37d396cf8f7a5ac32e97f36fcd4e02cff" } } ], "composite_release_requires_both_layers": true, "sqlite": { "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725", "filename": "nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite", "size_bytes": 37122048, "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "total_table_count": 120, "nonempty_table_count": 120, "hosting_path": "downloads/nmd-vcell-v1.2.0-measured-dmd-evidence-ro-crate.zip", "parts_manifest": "downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv", "hosting_status": "multipart_checksum_verified", "delivery": "embedded_in_portable_ro_crate", "archive_member": "database/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite", "source_parts_manifest": "downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv" }, "benchmark_summary": { "rmse_difference_vs_zero": { "estimator": "mean_across_repeated_balanced_fold_realizations", "mean": -0.006291882263806958, "ci95": [ -0.007352181034921496, -0.005240325481195381 ], "n_realizations": 20, "targets_per_realization": 2160, "bootstrap_replicates": 10000, "bootstrap_seed": 20260737, "source_object": "api/v1/v22_repeat_joint_uncertainty.json", "source_table": "downloads/v22_repeat_joint_uncertainty.tsv" }, "rmse_difference_vs_train_mean": { "estimator": "mean_across_repeated_balanced_fold_realizations", "mean": -0.0004662719641432719, "ci95": [ -0.0007022066115125746, -0.00022487605050965128 ], "n_realizations": 20, "targets_per_realization": 2160, "bootstrap_replicates": 10000, "bootstrap_seed": 20260737, "source_object": "api/v1/v22_repeat_joint_uncertainty.json", "source_table": "downloads/v22_repeat_joint_uncertainty.tsv" }, "raw_cosine_difference_vs_train_mean": { "estimator": "mean_across_repeated_balanced_fold_realizations", "mean": 0.0012235986991812387, "ci95": [ -0.00021601119406292822, 0.0024983961379381153 ], "n_realizations": 20, "targets_per_realization": 2160, "bootstrap_replicates": 10000, "bootstrap_seed": 20260737, "source_object": "api/v1/v22_repeat_joint_uncertainty.json", "source_table": "downloads/v22_repeat_joint_uncertainty.tsv" }, "perturbation_specific_residual_cosine": { "estimator": "mean_across_repeated_balanced_fold_realizations", "mean": 0.045280892411227326, "ci95": [ 0.02964996627740961, 0.06117821633174975 ], "n_realizations": 20, "targets_per_realization": 2160, "bootstrap_replicates": 10000, "bootstrap_seed": 20260737, "source_object": "api/v1/v22_repeat_joint_uncertainty.json", "source_table": "downloads/v22_repeat_joint_uncertainty.tsv" } }, "candidate_coverage": { "governed_hypotheses": 21, "observed_hepg2_perturbation": 21, "external_myoblast_context_assessed": 9, "independent_muscle_or_dmd_perturbation_replication": 0, "therapeutic_or_clinical_validation": 0 }, "v1_publication_target": { "target_schema": "nmd-vcell-v1-publication-target/1.0", "target_label": "formal_v1.0_database_paper_release", "candidate_status": "canonical_database_v1_release_object_identity_ready_external_gates_pending", "canonical_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "freeze_package_status": "canonical_object_identity_reconciled_formal_v1_locked", "formal_v1_release": false, "database_release_claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "database_paper_ready_when": [ "all internal public-object integrity checks pass", "both release layers are deposited under one permanent DOI record", "data licence and code licence are institution approved", "public maintainer, affiliation and contact metadata are author approved", "manuscript statements cite the exact release manifest, checksums, schema and claim boundary" ], "permitted_v1_claim": "versioned, citable, FAIR-oriented neuromuscular evidence workbench with static typed API, relational download, research-object registry, provenance, checksums and explicit claim boundaries", "not_authorized_claims": [ "validated DMD disease predictor", "therapeutic response predictor", "clinical decision-support platform", "treatment-prioritization engine" ], "paper_package_objects": [ "api/v1.1/release_manifest.json", "api/v1.1/openapi.json", "api/v1.3/research-objects/registry.json", "api/v1.4/project-state/DMD-MIN-PERTURBOME.json", "api/v1.1/v1_release_gate.json", "api/v1.1/v1_external_authorization_dossier.json", "api/v1.1/prediction_registry.json", "ro-crate-metadata.json", "codemeta.json", "checksums.sha256", "downloads/nmd_vcell_data_dictionary_schema_1.1.tsv", "downloads/DATABASE_PAPER_READINESS.md", "downloads/NAR_DATABASE_CHECKLIST.md", "downloads/DATA_AVAILABILITY.md", "downloads/MAINTENANCE_POLICY.md", "downloads/VERSIONING_POLICY.md", "downloads/V1_EXTERNAL_AUTHORIZATION_DOSSIER.md", "downloads/v1_deposit_manifest.json", "downloads/v1_deposit_file_list.tsv", "downloads/v1_authorization_checklist.tsv", "downloads/v1_licence_maintainer_metadata_template.tsv", "downloads/prediction_card.schema.json", "downloads/outcome_board.schema.json", "downloads/external_validation_import_template.json", "downloads/v1_release_handoff_checklist.tsv", "downloads/V1_EXTERNAL_GATE_HANDOFF.md", "downloads/v1_external_gate_input_template.json", "downloads/validate_v1_external_gates.py" ] }, "disease_prediction_readiness": { "readiness_schema": "nmd-vcell-disease-prediction-readiness/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "model_release": "ridge-safe-v2.3", "benchmark_protocol": "repeated-fold-v2.2", "current_level": "P0_prediction_infrastructure_only", "recommended_next_level": "P1_research_use_dmd_perturbation_response_prediction", "clinical_level_status": "P2_clinical_prediction_locked", "platform_claim_state": "P0_prediction_infrastructure_ready_P1_unvalidated_P2_locked", "allowed_current_claims": [ "static prediction-registration schema and empty registry are available", "same-HepG2 perturbation-response benchmark is auditable", "future prospective outcomes can be linked without overwriting predictions", "evidence gaps and abstention requirements are explicit" ], "locked_claims": [ "validated DMD disease predictor", "therapeutic response predictor", "clinical decision-support platform", "treatment-prioritization engine" ], "levels": [ { "level": "P0", "label": "Prediction infrastructure only", "status": "PASS", "claim_allowed": "registry, schema, benchmark and abstention infrastructure exist" }, { "level": "P1", "label": "Research-use DMD perturbation-response prediction", "status": "LOCKED_PENDING_EXTERNAL_VALIDATION", "claim_allowed": "none in this release" }, { "level": "P2", "label": "Clinical disease prediction or decision support", "status": "LOCKED_NOT_IN_SCOPE", "claim_allowed": "none" } ], "gate_summary": { "governed_hypotheses": 21, "observed_hepg2_perturbation": 21, "external_myoblast_context_assessed": 9, "independent_muscle_or_dmd_perturbation_replication": 0, "therapeutic_or_clinical_validation": 0, "prediction_registered": 0, "outcome_measured": 0 }, "p1_required_before_unlock": [ "frozen DMD/dystrophin-deficient human myogenic or neuromuscular perturbation dataset", "train/validation/external-test partition declared before model fitting", "donor, isogenic-pair or perturbation unit of analysis declared", "negative, positive and rescue/control definitions predeclared", "primary functional endpoint and transcriptomic secondary endpoints frozen", "baseline models, calibration, uncertainty intervals and abstention policy benchmarked", "out-of-distribution detection and failure-mode taxonomy frozen", "prospective prediction cards timestamped before outcome access", "outcome board populated without relabelling failed or abstained predictions" ], "p2_required_before_unlock": [ "clinical intended-use statement", "independent external clinical validation", "decision-impact or workflow evaluation protocol", "bias, safety, monitoring and human-oversight plan", "regulatory and ethics review appropriate to intended use" ], "minimum_validation_boundary": "No P1 or P2 prediction claim can be made until independent disease-relevant perturbation data, prospective registration, external test results, calibration, uncertainty, OOD and abstention analyses are frozen.", "reporting_alignment": [ "TRIPOD+AI-style model reporting fields are required before a P1 prediction claim", "DECIDE-AI/SPIRIT-AI/CONSORT-AI-style clinical evaluation fields are not triggered until a clinical workflow is proposed" ], "empty_registry_semantics": "Zero registered predictions and zero measured outcomes mean no qualifying prediction/outcome object exists; this is not a negative validation result." }, "v1_release_gate": { "gate_schema": "nmd-vcell-v1-release-gate/1.0", "resource_release": "v1.0.0-database-resource", "interface_build": "EA-20260802-46", "formal_v1_release": false, "freeze_status": "v1_final_release_freeze_candidate", "database_release_claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "candidate_status": "canonical_database_v1_release_object_identity_ready_external_gates_pending", "internal_gate_summary": { "pass": 10, "total": 10 }, "external_gate_summary": { "complete": 0, "pending": 4, "total": 4 }, "internal_gates": [ { "id": "single_source_release_identity", "status": "pass", "evidence": "api/v1.1/release_manifest.json" }, { "id": "analysis_core_archive_checksum", "status": "pass", "evidence": "checksums.sha256" }, { "id": "sqlite_integrity_and_nonempty_tables", "status": "pass", "evidence": "downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv" }, { "id": "typed_canonical_api", "status": "pass", "evidence": "api/v1.1/openapi.json" }, { "id": "bounded_candidate_decision_state", "status": "pass", "evidence": "api/v1.1/genes/GFOD2.json" }, { "id": "v1_release_freeze_gate", "status": "pass", "evidence": "api/v1.1/v1_release_gate.json" }, { "id": "prediction_registry_scaffold", "status": "pass", "evidence": "api/v1.1/prediction_registry.json" }, { "id": "database_paper_policy_package", "status": "pass", "evidence": "downloads/DATABASE_PAPER_READINESS.md" }, { "id": "external_authorization_dossier_package", "status": "pass", "evidence": "downloads/V1_EXTERNAL_AUTHORIZATION_DOSSIER.md" }, { "id": "evidence_atlas_overlay_archive_checksum", "status": "pass", "evidence": "api/v1.1/overlay_archive_identity.json" } ], "gate_categories": [ { "id": "file_checksum_integrity", "label": "File and checksum integrity", "status": "PASS", "scope": "Public release bytes and archive identities only", "evidence": "checksums.sha256" }, { "id": "api_schema_integrity", "label": "API and schema integrity", "status": "PASS", "scope": "Typed static objects and schema contracts only", "evidence": "api/v1.1/openapi.json" }, { "id": "cross_surface_project_state_consistency", "label": "Cross-page project-state consistency", "status": "PASS", "scope": "Stage A assignment, freeze, registration and outcome state", "evidence": "api/v1.4/project-state/DMD-MIN-PERTURBOME.json" }, { "id": "legal_release_identity", "label": "Legal and release identity", "status": "PENDING", "scope": "DOI, licences, maintainer and institutional authorization", "evidence": "api/v1.1/v1_external_authorization_dossier.json" }, { "id": "scientific_prediction_validity", "label": "Scientific prediction validity", "status": "LOCKED", "scope": "Independent DMD perturbation truth, calibration and prospective outcomes", "evidence": "api/v1.1/prediction_readiness.json" }, { "id": "independent_user_e2e", "label": "Independent user reconstruction", "status": "PARTIAL", "scope": "Local route QA passes; independent clean-room reconstruction remains incomplete", "evidence": "api/v1.3/research-objects/reproducibility.json" } ], "external_gates": [ { "id": "permanent_doi_archive", "status": "pending_external_action", "required_input": "DOI for the unchanged canonical archive" }, { "id": "institution_approved_data_licence", "status": "pending_institutional_approval", "required_input": "Approved data licence identifier and text" }, { "id": "approved_code_licence", "status": "pending_institutional_approval", "required_input": "Approved code licence identifier and text" }, { "id": "final_maintainer_and_institution_metadata", "status": "pending_author_input", "required_input": "Approved maintainer, affiliation and contact metadata" } ], "publication_package": [ "api/v1.1/release_manifest.json", "api/v1.1/openapi.json", "api/v1.3/research-objects/registry.json", "api/v1.4/project-state/DMD-MIN-PERTURBOME.json", "api/v1.1/v1_release_gate.json", "api/v1.1/v1_external_authorization_dossier.json", "api/v1.1/prediction_registry.json", "ro-crate-metadata.json", "codemeta.json", "checksums.sha256", "downloads/nmd_vcell_data_dictionary_schema_1.1.tsv", "downloads/DATABASE_PAPER_READINESS.md", "downloads/NAR_DATABASE_CHECKLIST.md", "downloads/DATA_AVAILABILITY.md", "downloads/MAINTENANCE_POLICY.md", "downloads/VERSIONING_POLICY.md", "downloads/V1_EXTERNAL_AUTHORIZATION_DOSSIER.md", "downloads/v1_deposit_manifest.json", "downloads/v1_deposit_file_list.tsv", "downloads/v1_authorization_checklist.tsv", "downloads/v1_licence_maintainer_metadata_template.tsv", "downloads/prediction_card.schema.json", "downloads/outcome_board.schema.json", "downloads/external_validation_import_template.json", "downloads/v1_release_handoff_checklist.tsv", "downloads/V1_EXTERNAL_GATE_HANDOFF.md", "downloads/v1_external_gate_input_template.json", "downloads/validate_v1_external_gates.py" ], "claim_boundary_enforced_on_pages": [ "index.html", "release.html", "v1_release_gate.html", "v1_authorization.html", "prediction_readiness.html", "prediction_registry.html", "api/v1.1/release_manifest.json", "api/v1.1/openapi.json", "api/v1.3/research-objects/registry.json", "api/v1.4/project-state/DMD-MIN-PERTURBOME.json", "ro-crate-metadata.json" ], "prediction_claim_state": "P0_prediction_infrastructure_ready_P1_unvalidated_P2_locked", "unlock_rule": "Only after all four external gates are structurally complete and author/institution authorization is recorded may the site label be changed to formal v1.0. That change still does not unlock P1 or P2 prediction claims." }, "v1_external_authorization_dossier": { "dossier_schema": "nmd-vcell-v1-external-authorization-dossier/1.0", "resource_release": "v1.0.0-database-resource", "interface_build": "EA-20260802-46", "formal_v1_release": false, "dossier_status": "ready_for_author_institution_input_formal_v1_locked", "database_release_claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "external_gate_summary": { "complete": 0, "pending": 4, "total": 4 }, "required_external_inputs": [ { "gate_id": "permanent_doi_archive", "status": "pending_external_action", "required_input": "DOI for the unchanged canonical archive" }, { "gate_id": "institution_approved_data_licence", "status": "pending_institutional_approval", "required_input": "Approved data licence identifier and text" }, { "gate_id": "approved_code_licence", "status": "pending_institutional_approval", "required_input": "Approved code licence identifier and text" }, { "gate_id": "final_maintainer_and_institution_metadata", "status": "pending_author_input", "required_input": "Approved maintainer, affiliation and contact metadata" } ], "deposit_manifest": "downloads/v1_deposit_manifest.json", "deposit_file_list": "downloads/v1_deposit_file_list.tsv", "authorization_checklist": "downloads/v1_authorization_checklist.tsv", "input_template": "downloads/v1_external_gate_input_template.json", "metadata_template": "downloads/v1_licence_maintainer_metadata_template.tsv", "validator": "downloads/validate_v1_external_gates.py", "handoff": "downloads/V1_EXTERNAL_GATE_HANDOFF.md", "page": "v1_authorization.html", "privacy_boundary": "Do not publish maintainer email, affiliation details or approval metadata until the author/institution has explicitly approved the public values.", "non_automated_actions": [ "mint DOI for the unchanged two-layer release package", "obtain institution-approved data licence identifier and text", "obtain institution-approved code licence identifier and text", "obtain author-approved maintainer, affiliation and contact metadata", "record formal release authorization person and ISO-8601 timestamp" ], "automatic_unlock": false, "release_layers": [ { "layer": "analysis_core", "required_for_composite_release": true, "archive": { "object_id": "FILE:CORE:v0.8.1:v24r1:20260722", "filename": "nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz", "size_bytes": 9677910, "sha256": "b88a3b9f1ae44b48d6ea3c2a568626229cc93f94d539b8ea30f55534aae41f36" } }, { "layer": "evidence_atlas_overlay", "required_for_composite_release": true, "archive": { "object_id": "FILE:OVERLAY:v1.0.0-database-resource:stage5.88:20260802", "filename": "nmd_vcell_research_workbench_overlay_v1.0.0_database_resource_20260802_stage5_88.tar.gz", "size_bytes": 3178743, "sha256": "04c982d002b3ab0ad44319d6327116086da3a87a182430e4d475a1e2ad60b2e1" } } ] }, "prediction_registry": { "registry_schema": "nmd-vcell-prediction-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "interface_build": "EA-20260817-57", "registry_status": "empty_scaffold_no_predictions_registered", "claim_state": "P0_prediction_infrastructure_ready_P1_unvalidated_P2_locked", "counts": { "prediction_registered": 0, "outcome_measured": 0, "abstained_predictions": 0, "failed_predictions": 0, "passed_predictions": 0 }, "schemas": { "prediction_card": "downloads/prediction_card.schema.json", "outcome_board": "downloads/outcome_board.schema.json", "external_validation_import_template": "downloads/external_validation_import_template.json" }, "records": [], "outcomes": [], "empty_registry_semantics": "No prediction has been prospectively registered and no outcome has been measured in this release. The empty registry is an integrity state, not evidence of model failure or success.", "p1_unlock_requires": [ "frozen DMD/dystrophin-deficient human myogenic or neuromuscular perturbation dataset", "train/validation/external-test partition declared before model fitting", "donor, isogenic-pair or perturbation unit of analysis declared", "negative, positive and rescue/control definitions predeclared", "primary functional endpoint and transcriptomic secondary endpoints frozen", "baseline models, calibration, uncertainty intervals and abstention policy benchmarked", "out-of-distribution detection and failure-mode taxonomy frozen", "prospective prediction cards timestamped before outcome access", "outcome board populated without relabelling failed or abstained predictions" ], "p2_unlock_requires": [ "clinical intended-use statement", "independent external clinical validation", "decision-impact or workflow evaluation protocol", "bias, safety, monitoring and human-oversight plan", "regulatory and ethics review appropriate to intended use" ], "not_authorized_claims": [ "validated DMD disease predictor", "therapeutic response predictor", "clinical decision-support platform", "treatment-prioritization engine" ] }, "measured_dmd_evidence": { "object_id": "MDE:v1.2.0-measured-dmd-evidence:EA-20260817-57", "release_state": "RELEASED_MEASURED_DMD_CONTEXT_CANDIDATE_PREDICTION_LOCKED", "api": "api/v1.6/measured-dmd-evidence/summary.json", "page": "measured-dmd-evidence/", "cleanroom_reproducibility": { "status": "PASS", "checks": { "checks": 16, "passed": 16, "failed": 0 }, "api": "cleanroom-reproducibility.json", "report": "/resource/downloads/CLEANROOM_MEASURED_DMD_REPRODUCIBILITY_REPORT_v1.md", "isolation_boundary": "Fresh path-isolated workspace and process environment; system Python/R packages reused, not a container or independently administered host." }, "candidate_dmd_response_outcomes": "0/21", "candidate_dmd_response_truth": "0/21", "candidate_level_dmd_pathway_predictions": 0 }, "claim_boundary": "L1 resource records and L2 same-HepG2 observed perturbation evidence, selected L3a external-context screens, measured DMD-locus induction and correction, and sample-level external disease pathway analyses. No candidate-level DMD perturbation truth, calibrated candidate pathway prediction, L5 therapeutic evidence or clinical evidence is present. v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "formal_v1_release": false, "release_readiness": { "status": "public_object_integrity_pass_external_and_scientific_gates_open", "formal_v1_ready": false, "freeze_package_status": "canonical_object_identity_reconciled_formal_v1_locked", "database_release_claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "external_gate_input_contract": { "template": "downloads/v1_external_gate_input_template.json", "validator": "downloads/validate_v1_external_gates.py", "instructions": "downloads/V1_EXTERNAL_GATE_HANDOFF.md", "automatic_formal_release": false }, "internal_gates": [ { "id": "single_source_release_identity", "status": "pass", "evidence": "api/v1.1/release_manifest.json" }, { "id": "analysis_core_archive_checksum", "status": "pass", "evidence": "checksums.sha256" }, { "id": "sqlite_integrity_and_nonempty_tables", "status": "pass", "evidence": "downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv" }, { "id": "typed_canonical_api", "status": "pass", "evidence": "api/v1.1/openapi.json" }, { "id": "bounded_candidate_decision_state", "status": "pass", "evidence": "api/v1.1/genes/GFOD2.json" }, { "id": "v1_release_freeze_gate", "status": "pass", "evidence": "api/v1.1/v1_release_gate.json" }, { "id": "prediction_registry_scaffold", "status": "pass", "evidence": "api/v1.1/prediction_registry.json" }, { "id": "database_paper_policy_package", "status": "pass", "evidence": "downloads/DATABASE_PAPER_READINESS.md" }, { "id": "external_authorization_dossier_package", "status": "pass", "evidence": "downloads/V1_EXTERNAL_AUTHORIZATION_DOSSIER.md" }, { "id": "evidence_atlas_overlay_archive_checksum", "status": "pass", "evidence": "api/v1.1/overlay_archive_identity.json" } ], "gate_categories": [ { "id": "file_checksum_integrity", "label": "File and checksum integrity", "status": "PASS", "scope": "Public release bytes and archive identities only", "evidence": "checksums.sha256" }, { "id": "api_schema_integrity", "label": "API and schema integrity", "status": "PASS", "scope": "Typed static objects and schema contracts only", "evidence": "api/v1.1/openapi.json" }, { "id": "cross_surface_project_state_consistency", "label": "Cross-page project-state consistency", "status": "PASS", "scope": "Stage A assignment, freeze, registration and outcome state", "evidence": "api/v1.4/project-state/DMD-MIN-PERTURBOME.json" }, { "id": "legal_release_identity", "label": "Legal and release identity", "status": "PENDING", "scope": "DOI, licences, maintainer and institutional authorization", "evidence": "api/v1.1/v1_external_authorization_dossier.json" }, { "id": "scientific_prediction_validity", "label": "Scientific prediction validity", "status": "LOCKED", "scope": "Independent DMD perturbation truth, calibration and prospective outcomes", "evidence": "api/v1.1/prediction_readiness.json" }, { "id": "independent_user_e2e", "label": "Independent user reconstruction", "status": "PARTIAL", "scope": "Local route QA passes; independent clean-room reconstruction remains incomplete", "evidence": "api/v1.3/research-objects/reproducibility.json" } ], "external_gates": [ { "id": "permanent_doi_archive", "status": "pending_external_action", "required_input": "DOI for the unchanged canonical archive" }, { "id": "institution_approved_data_licence", "status": "pending_institutional_approval", "required_input": "Approved data licence identifier and text" }, { "id": "approved_code_licence", "status": "pending_institutional_approval", "required_input": "Approved code licence identifier and text" }, { "id": "final_maintainer_and_institution_metadata", "status": "pending_author_input", "required_input": "Approved maintainer, affiliation and contact metadata" } ] }, "external_release_gates": [ "permanent_doi_archive", "institution_approved_data_licence", "approved_code_licence", "final_maintainer_and_institution_metadata" ], "external_release_gate_status": { "approved_code_licence": "pending_external_gate", "final_maintainer_and_institution_metadata": "pending_external_gate", "institution_approved_data_licence": "pending_external_gate", "permanent_doi_archive": "pending_external_gate" }, "additive_multidisease_module": { "module_release": "multidisease-evidence-v0.2.0", "status": "ADDITIVE_EVIDENCE_MODULE_NO_PARENT_CLAIM_EXPANSION", "manifest": "/resource/api/v2/diseases/manifest.json", "diseases": [ "DMD", "FSHD", "DM1", "SMA" ], "disease_routes": 4, "previous_release": "/resource/api/v2/releases/multidisease-evidence-v0.1.0/diseases/manifest.json", "claim_boundary": "Disease-specific measured, induced, corrected, perturbed and missing evidence; no common calibrated predictor, patient simulation, treatment ranking or clinical recommendation." }, "canonical_database_v1_release_bundle": { "bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "candidate_resource_version": "v1.0.0-database-resource", "candidate_status": "metadata_identity_candidate_not_formal_release", "doi": "DOI_PENDING", "formal_v1_release": false, "license": "LICENSE_PENDING_INSTITUTIONAL_APPROVAL", "objects": [ { "delivery": "single_file", "object_id": "FILE:CORE:v0.8.1:v24r1:20260722", "object_role": "analysis_core_archive", "path": "deploy/nmd-vcell-site/public/resource/downloads/nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz", "sha256": "b88a3b9f1ae44b48d6ea3c2a568626229cc93f94d539b8ea30f55534aae41f36", "size_bytes": 9677910, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" }, { "delivery": "single_file", "object_id": "FILE:OVERLAY:v1.0.0-database-resource:stage5.88:20260802", "object_role": "evidence_atlas_overlay_archive", "path": "deploy/nmd-vcell-site/public/resource/downloads/nmd_vcell_research_workbench_overlay_v1.0.0_database_resource_20260802_stage5_88.tar.gz", "sha256": "04c982d002b3ab0ad44319d6327116086da3a87a182430e4d475a1e2ad60b2e1", "size_bytes": 3178743, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" }, { "delivery": "single_file", "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725", "object_role": "sqlite_schema1.1_relational_payload", "path": "results/public_resource_post416i_local_candidate_20260724/database/nmd_vcell_public_resource.sqlite", "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "size_bytes": 37122048, "sqlite_nonempty_table_count": 120, "sqlite_total_table_count": 120 }, { "delivery": "multipart", "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725:HOSTED_PARTS", "object_role": "hosted_sqlite_multipart_delivery", "path": "deploy/nmd-vcell-site/public/resource/downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv", "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "size_bytes": 37122048, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" } ], "schema": "nmd_vcell.canonical_release_bundle_reference.v1", "source_stage": "submission_nar_database/stage5_24_canonical_release_object_identity_reconciliation/04_canonical_database_v1_release_bundle_candidate.json" }, "database_v1_release_object_identity_candidate": { "allowed_scope": "database_v1_release_object_identity_only_no_final_unlock_no_prediction_claim_expansion", "blocked_until": [ "EXTGATE-V1-003 license/stewardship approval", "EXTGATE-V1-005 normal/private browser QA", "EXTGATE-V1-006 DOI/archive deposition and post-DOI checksum freeze", "EXTGATE-V1-007 external submission/release authority", "EXTGATE-V1-008 portable environment lock or accepted rerun evidence", "EXTGATE-V1-009 independent external-user evaluation", "EXTGATE-V1-012 final database-v1 unlock signoff" ], "bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "candidate_resource_version": "v1.0.0-database-resource", "canonical_objects": [ { "delivery": "single_file", "object_id": "FILE:CORE:v0.8.1:v24r1:20260722", "object_role": "analysis_core_archive", "path": "deploy/nmd-vcell-site/public/resource/downloads/nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz", "sha256": "b88a3b9f1ae44b48d6ea3c2a568626229cc93f94d539b8ea30f55534aae41f36", "size_bytes": 9677910, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" }, { "delivery": "single_file", "object_id": "FILE:OVERLAY:v1.0.0-database-resource:stage5.88:20260802", "object_role": "evidence_atlas_overlay_archive", "path": "deploy/nmd-vcell-site/public/resource/downloads/nmd_vcell_research_workbench_overlay_v1.0.0_database_resource_20260802_stage5_88.tar.gz", "sha256": "04c982d002b3ab0ad44319d6327116086da3a87a182430e4d475a1e2ad60b2e1", "size_bytes": 3178743, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" }, { "delivery": "single_file", "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725", "object_role": "sqlite_schema1.1_relational_payload", "path": "results/public_resource_post416i_local_candidate_20260724/database/nmd_vcell_public_resource.sqlite", "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "size_bytes": 37122048, "sqlite_nonempty_table_count": 120, "sqlite_total_table_count": 120 }, { "delivery": "multipart", "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725:HOSTED_PARTS", "object_role": "hosted_sqlite_multipart_delivery", "path": "deploy/nmd-vcell-site/public/resource/downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv", "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "size_bytes": 37122048, "sqlite_nonempty_table_count": "", "sqlite_total_table_count": "" } ], "canonical_sqlite_schema11": { "delivery": "single_file", "object_id": "FILE:SQLITE:v0.9.2:schema1.1:20260725", "object_role": "sqlite_schema1.1_relational_payload", "path": "results/public_resource_post416i_local_candidate_20260724/database/nmd_vcell_public_resource.sqlite", "sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "size_bytes": 37122048, "sqlite_nonempty_table_count": 120, "sqlite_total_table_count": 120 }, "claim_boundary": "v1.0 is a database and evidence-governance release; it is not a validated disease-prediction or clinical decision-support release.", "created_at_iso": "2026-07-26T09:43:49.038653+00:00", "created_by_stage": "stage5_25_exact_metadata_identity_patch_candidates", "doi": "DOI_PENDING", "formal_v1_release": false, "hosted_sqlite_parts": { "aggregate_sha256": "874377d932b67b8ce3254db27ec9f483db6d9a11d90a929e7369ce6eb131ef27", "aggregate_size_bytes": 37122048, "part_count": 5, "parts_manifest": "deploy/nmd-vcell-site/public/resource/downloads/large_assets/nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite/parts_manifest.tsv", "parts_status": "PASS_PARTS_MATCH_MANIFEST" }, "license": "LICENSE_PENDING_INSTITUTIONAL_APPROVAL", "prediction_platform_claim_state": "P0_prediction_infrastructure_ready_P1_unvalidated_P2_locked", "resource_name": "NMD-VCell", "schema": "nmd_vcell.database_v1_release_object_identity_candidate.v1", "stage5_24_bundle_path": "submission_nar_database/stage5_24_canonical_release_object_identity_reconciliation/04_canonical_database_v1_release_bundle_candidate.json", "stage5_24_bundle_sha256": "cf54f477fa4034a2c15f296a204e8ababad53c2870102664f18817fc90bbe4e3", "status": "candidate_metadata_identity_only_not_formal_v1_not_deposited", "submission_ready": false }, "current_release_composite_digest_sha256": "873e7c59fe40c8eb6d5bdacfd887f319e2fec38ee397fc983236ddbc4c5498b4", "base_publication_bundle_identity_digest_sha256": "b435f2100badd88e81dae1afa47bff278ba97d56d84df6d5d4dd6c3d4096b256", "release_identity_policy": "canonical_bundle_identity_digest_sha256 identifies the immutable database-v1 publication base; current_release_composite_digest_sha256 identifies the current analysis-core, SQLite and successor-overlay set.", "overlay_archive": { "object_id": "FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.106:20260904", "filename": "nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_106.tar.gz", "size_bytes": 7206687, "sha256": "3733a936e8ba0d0da7336e3d5631b1b37d396cf8f7a5ac32e97f36fcd4e02cff", "role": "research_workbench_overlay_archive", "layer_release": "v1.2.0-measured-dmd-evidence", "scope_manifest_inside_archive": "OVERLAY_ARCHIVE_SCOPE.json", "size_bound_direct_public_object_count": 36, "coverage": "Current Workbench interface, research-object contracts, Study Cards, schemas, selected audit/build scripts and checksummed derived-object references; requires the analysis-core layer, source repository, declared dependencies and governed external-workspace inputs for a full rebuild." } }