{ "registry_schema": "nmd-vcell-research-landscape/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "route": "/resource/landscape/", "asset_inventory": { "inventory_schema": "nmd-vcell-research-asset-inventory/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "headline": "The workspace contains substantially more research and visual material than the formal website registries expose.", "counts": { "controlled_public_routes": 161, "formally_registered_datasets": 5, "model_cards": 5, "frozen_model_runs": 6, "calibrated_dmd_models": 0, "current_curated_main_figures": 9, "current_curated_supplementary_figures": 27, "current_curated_supplementary_tables": 44, "historical_visual_asset_instances": 1707, "historical_unique_visual_hashes": 773, "public_publication_and_figure_download_assets": 69 }, "records": [ { "asset_id": "ASSET-PUBLIC-PRODUCT", "asset_class": "PUBLIC_PRODUCT", "lifecycle_state": "RELEASED", "title": "Controlled public website and typed API", "inventory": "161 controlled routes with release, route and checksum manifests", "public_entrypoint": "/resource/", "source_object": "/resource/api/v1.1/route_manifest.json", "current_gap": "A route inventory existed, but research assets, external opportunities and adoption decisions were not presented in one navigable view.", "action": "Keep this landscape page in the controlled route and release manifests." }, { "asset_id": "ASSET-DATA-MODEL-REGISTRIES", "asset_class": "COMPUTABLE_REGISTRIES", "lifecycle_state": "RELEASED_LIMITED", "title": "Typed dataset, model-card and ModelRun registries", "inventory": "5 datasets · 5 model cards · 6 frozen runs · 0 calibrated DMD models", "public_entrypoint": "/resource/models/", "source_object": "/resource/api/v1.1/model_run_registry.json", "current_gap": "The execution ledger is strong, but disease-relevant perturbation outcomes and author-missing feature/metadata files remain absent.", "action": "Acquire missing metadata first; evaluate new adapters on compatible non-DMD benchmarks before any disease claim." }, { "asset_id": "ASSET-CURATED-V06-PUBLICATION", "asset_class": "PUBLICATION_PACKAGE", "lifecycle_state": "CURATED_NOT_SUBMISSION_READY", "title": "Curated v06 manuscript, main figures and supplement", "inventory": "9 main figures · 27 supplementary figures · 44 supplementary tables · 36 traced figure artifacts · 16 traced key numeric claims", "public_entrypoint": "/resource/downloads/multidisease-v02/NMD_VCell_NAR_Manuscript_curated_v06_WORKING.pdf", "source_object": "/resource/downloads/multidisease-v02/CURATED_V06_VERIFICATION.json", "current_gap": "Technical verification passes, while the pre-submission integrity state remains blocked and the package is explicitly working material.", "action": "Expose the current package and its verification state without hiding v05 or claiming submission readiness." }, { "asset_id": "ASSET-HISTORICAL-VISUAL-LINEAGE", "asset_class": "HISTORICAL_VISUAL_LINEAGE", "lifecycle_state": "HISTORICAL_PRESERVED", "title": "All-version visual asset lineage", "inventory": "1,707 visual asset instances · 773 unique SHA-256 values · 1.187 GB audited source lineage", "public_entrypoint": "/resource/api/v1.1/research_asset_inventory.json", "source_object": "curated_v06/source_registry/ALL_VERSION_VISUAL_ASSET_SUMMARY.json (workspace audit source)", "current_gap": "Historical assets were retained in the workspace but were not discoverable from the public product.", "action": "Preserve every predecessor and publish selection lineage; do not replace historical assets with only the current render." }, { "asset_id": "ASSET-MULTIDISEASE-ATLAS", "asset_class": "DISEASE_EVIDENCE", "lifecycle_state": "RELEASED_WITH_SCOPE_DIFFERENCES", "title": "DMD, FSHD, DM1 and SMA evidence atlas", "inventory": "4 disease modules and 10 measured-or-missing cell-context records under one evidence vocabulary", "public_entrypoint": "/resource/diseases/", "source_object": "/resource/api/v2/diseases/manifest.json", "current_gap": "Disease evidence depth differs and cannot be collapsed into a shared predictor or disease ranking.", "action": "Extend donor-resolved cell objects only when source metadata and statistical units pass registration." }, { "asset_id": "ASSET-DMD-PERTURBATION-OUTCOME", "asset_class": "DECISION_CRITICAL_MISSING_ASSET", "lifecycle_state": "MISSING", "title": "Independent candidate-level DMD perturbation outcomes", "inventory": "0/21 governed candidates with qualifying independent DMD perturbation outcomes", "public_entrypoint": "/resource/prediction_readiness", "source_object": "/resource/api/v1.6/measured-dmd-evidence/candidate-outcome-boundary.json", "current_gap": "No released dataset can calibrate a candidate-level DMD response predictor.", "action": "Keep DMD perturbation prediction locked; computational expansion cannot manufacture this missing outcomes." } ], "interpretation": "The visible shortage was primarily an indexing and product-organization problem, not wholesale deletion. Historical assets remain preserved; current release objects and missing scientific outcomes must still be distinguished.", "claim_boundary": "Asset presence, curation or technical verification does not establish biological validation, model calibration or submission readiness." }, "competitive_landscape": { "registry_schema": "nmd-vcell-competitive-landscape/1.1", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "reference_count": 14, "evidence_rule": "Competitor descriptions are design references verified against official or primary sources. Their data scale, model performance and product capability are not inherited by NMD-VCell.", "segmentation_axes": [ "competitor_type", "primary_user", "entry_task", "moat", "openness", "wet_lab_loop", "disease_specificity", "evidence_transparency", "adoption_priority" ], "records": [ { "reference_id": "LANDSCAPE-ARC-VCI", "platform": "Arc Virtual Cell Initiative · STATE · Stack · VCC", "category": "FULL_STACK_VIRTUAL_CELL", "observed_capability": "Connects large observational and perturbational atlases, open models, standardized evaluation and a held-out challenge. Stack adds in-context single-cell modeling; the 2025 challenge retained simple baselines and exposed generalization failures.", "practice_to_adopt": "Bind every prediction to a frozen task, hidden or sealed outcomes, permanent simple baselines and a ModelRun record.", "nmd_vcell_advantage": "Disease-specific evidence governance, explicit missing outcomes, candidate Study Cards and preservation of negative runs.", "current_gap": "No Arc-scale training corpus, no locally executed STATE or Stack adapter and no disease-relevant held-out perturbation outcomes.", "adoption_state": "PARTIAL_PRACTICE_ADOPTED_MODEL_NOT_INHERITED", "sources": [ { "title": "Arc Virtual Cell Initiative", "url": "https://arcinstitute.org/virtual-cell-initiative", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Stack release", "url": "https://arcinstitute.org/news/foundation-model-stack", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "VCC 2025 wrap-up", "url": "https://arcinstitute.org/news/virtual-cell-challenge-2025-wrap-up", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "ML developers and computational biologists", "entry_task": "Train or benchmark a perturbation model", "moat": "DATA_MODEL_BENCHMARK", "openness": "OPEN_RESEARCH", "wet_lab_loop": "PARTIAL", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "HIGH", "adoption_priority": "P0", "practice_not_to_copy": "Do not present Arc-scale data, leaderboards or generalization as local capability.", "local_equivalent": [ "Data Universe", "ModelRun registry", "Benchmark dashboard" ] }, { "reference_id": "LANDSCAPE-CZI-VCP", "platform": "CZI / Biohub Virtual Cells Platform", "category": "MODEL_DATA_BENCHMARK_PLATFORM", "observed_capability": "Publishes model cards, datasets, benchmarks, CLI access and hosted workflows in one ecosystem, including TranscriptFormer and the context-specific scLDM.CD4 perturbation model.", "practice_to_adopt": "Use one adapter and metadata contract across data discovery, local execution, benchmark reporting and web presentation.", "nmd_vcell_advantage": "A narrower neuromuscular decision loop with explicit claim ceilings and source-to-experiment traceability.", "current_gap": "NMD-VCell has a run ledger but not a unified executable adapter layer or hosted inference workspace.", "adoption_state": "MODEL_RUN_LEDGER_RELEASED_ADAPTER_LAYER_NEXT", "sources": [ { "title": "Virtual Cells Platform", "url": "https://virtualcellmodels.cziscience.com/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Virtual Cells benchmarks", "url": "https://virtualcellmodels.cziscience.com/benchmarks", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Models catalog", "url": "https://virtualcellmodels.cziscience.com/models", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "Biologists and ML developers", "entry_task": "Find data, select a model, run or compare", "moat": "MODEL_DATA_BENCHMARK_WORKSPACE", "openness": "OPEN_PLATFORM", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "HIGH", "adoption_priority": "P0", "practice_not_to_copy": "Do not build a broad model marketplace before disease workflows and adapters are stable.", "local_equivalent": [ "Dataset registry", "Model cards", "ModelRun registry", "Virtual Cell Studio" ] }, { "reference_id": "LANDSCAPE-CELLXGENE", "platform": "CZ CELLxGENE Discover · Explorer · Census", "category": "SINGLE_CELL_DATA_PLATFORM", "observed_capability": "Provides versioned, ontology-harmonized single-cell data with low-latency metadata queries, source H5AD access and interoperable AnnData, Seurat and SingleCellExperiment slices.", "practice_to_adopt": "Make dataset, donor, disease, state, batch and gene selections resolve to stable source objects and exportable analysis units.", "nmd_vcell_advantage": "Neuromuscular disease interpretation and donor-aware claim ceilings rather than a general atlas browser.", "current_gap": "The current Cell Context Explorer is a typed context registry, not yet a donor-level cell browser over imported matrices.", "adoption_state": "CONTEXT_REGISTRY_RELEASED_CELL_OBJECT_IMPORT_NEXT", "sources": [ { "title": "CELLxGENE Census", "url": "https://chanzuckerberg.github.io/cellxgene-census/index", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "CELLxGENE product documentation", "url": "https://cellxgene.cziscience.com/docs/01__CellxGene", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "ADJACENT", "primary_user": "Single-cell biologists", "entry_task": "Find and explore a cell dataset", "moat": "STANDARDIZED_DATA_DISCOVERY", "openness": "OPEN_PLATFORM", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "HIGH", "adoption_priority": "P1", "practice_not_to_copy": "Do not treat cell counts as independent biological replication.", "local_equivalent": [ "Cell Context Map", "Dataset registry" ] }, { "reference_id": "LANDSCAPE-OPEN-TARGETS", "platform": "Open Targets Platform", "category": "TARGET_DISEASE_ENTITY_GRAPH", "observed_capability": "Exposes source-provenanced target, disease, drug and association entities through a web interface, downloads, GraphQL and a versioned official MCP server.", "practice_to_adopt": "Keep stable entity identifiers, release metadata, source-level provenance and machine interfaces synchronized.", "nmd_vcell_advantage": "Cell-context, perturbation-run and prospective-study objects specialized for neuromuscular research.", "current_gap": "NMD-VCell has linked objects but lacks a general graph query or agent interface across every object type.", "adoption_state": "PARTIAL_OBJECT_GRAPH_RELEASED_QUERY_LAYER_NEXT", "sources": [ { "title": "Open Targets Platform", "url": "https://platform.opentargets.org/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Open Targets GraphQL API", "url": "https://api.platform.opentargets.org/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Open Targets MCP", "url": "https://mcp.platform.opentargets.org/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "ADJACENT", "primary_user": "Target and translational researchers", "entry_task": "Inspect a target–disease relationship", "moat": "ENTITY_RELATION_EVIDENCE", "openness": "OPEN_PLATFORM", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_DISEASE", "evidence_transparency": "HIGH", "adoption_priority": "P0", "practice_not_to_copy": "Do not collapse heterogeneous evidence into one opaque target score.", "local_equivalent": [ "Gene records", "Disease atlas", "Evidence graph" ] }, { "reference_id": "LANDSCAPE-DEPMAP", "platform": "DepMap Portal", "category": "FUNCTIONAL_DEPENDENCY_PLATFORM", "observed_capability": "Combines recurring public CRISPR dependency releases, molecular characterization, model metadata, downloads and experimental APIs.", "practice_to_adopt": "Version data releases, model contexts and mapping files together, and expose historical release identities.", "nmd_vcell_advantage": "Disease-specific evidence boundaries prevent cancer-cell dependency from being relabeled as muscle efficacy.", "current_gap": "DepMap can add contextual dependency evidence, but it is not direct DMD muscle perturbation outcome.", "adoption_state": "REFERENCE_DATA_ONLY_NO_DMD_INHERITANCE", "sources": [ { "title": "DepMap Public 26Q1 data", "url": "https://depmap.org/portal/data_page/?tab=allData", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "DepMap APIs", "url": "https://depmap.org/portal/api/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "ADJACENT", "primary_user": "Functional genomics researchers", "entry_task": "Query dependency in a model context", "moat": "RECURRING_FUNCTIONAL_DATA", "openness": "OPEN_DATA_PORTAL", "wet_lab_loop": "PARTIAL", "disease_specificity": "CANCER", "evidence_transparency": "HIGH", "adoption_priority": "P2", "practice_not_to_copy": "Do not relabel cancer-cell dependency as neuromuscular efficacy.", "local_equivalent": [ "External context evidence", "Source buckets" ] }, { "reference_id": "LANDSCAPE-VITESSCE", "platform": "Vitessce", "category": "LINKED_SINGLE_CELL_VISUALIZATION", "observed_capability": "Uses JSON view configurations to coordinate embeddings, expression matrices, spatial images and controls over static or object-store data.", "practice_to_adopt": "Add linked gene, cell-state, donor, heatmap and spatial views after qualified AnnData-Zarr objects are registered.", "nmd_vcell_advantage": "The visual layer would inherit NMD-VCell evidence states and donor-aware statistical rules.", "current_gap": "No production AnnData-Zarr or Vitessce view configuration is registered for DMD tissue data.", "adoption_state": "VISUAL_PATTERN_VERIFIED_DATA_PREPARATION_BLOCKED", "sources": [ { "title": "Vitessce documentation", "url": "https://vitessce.io/docs/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "INFRASTRUCTURE", "primary_user": "Single-cell and spatial analysts", "entry_task": "Compose linked views over registered objects", "moat": "LINKED_VISUAL_CONFIGURATION", "openness": "OPEN_SOURCE", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "MEDIUM", "adoption_priority": "P2", "practice_not_to_copy": "Do not add a viewer before donor-aware, checksum-addressed objects exist.", "local_equivalent": [ "Future linked cell browser" ] }, { "reference_id": "LANDSCAPE-VCELL", "platform": "VCell Modeling & Analysis Software", "category": "MECHANISTIC_SIMULATION", "observed_capability": "Separates biological model definition, applications, parameters, geometry, numerical solvers, simulation runs and downloadable results across deterministic and stochastic methods.", "practice_to_adopt": "Keep evidence checks, learned response models and future mechanistic solvers as distinct object classes with equations, parameters and run logs.", "nmd_vcell_advantage": "NMD-VCell begins from disease evidence and the experiment needed to establish a modelable transition.", "current_gap": "No calibrated mechanistic DMD model, parameter set or numerical simulation result is released.", "adoption_state": "OBJECT_SEPARATION_ADOPTED_SOLVER_LAYER_LOCKED", "sources": [ { "title": "VCell platform", "url": "https://vcell.org/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "VCell source repository", "url": "https://github.com/virtualcell/vcell", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "ADJACENT", "primary_user": "Systems and computational biologists", "entry_task": "Build and simulate a mechanistic model", "moat": "MECHANISTIC_SIMULATION", "openness": "OPEN_SOURCE", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "HIGH", "adoption_priority": "P2", "practice_not_to_copy": "Do not relabel an evidence graph as a calibrated mechanistic simulation.", "local_equivalent": [ "DMD process map", "Future mechanistic solver lane" ] }, { "reference_id": "LANDSCAPE-TAHOE", "platform": "Tahoe · Mosaic · Tahoe-100M", "category": "PERTURBATION_DATA_ENGINE", "observed_capability": "Builds large perturbational single-cell maps and publishes Tahoe-100M as a reusable data product with manuscript, download, community and model entry points.", "practice_to_adopt": "Treat every important disease dataset as a versioned product with a scientific question, access path, limitations, examples and downstream model links.", "nmd_vcell_advantage": "NMD-VCell can make donor structure, neuromuscular context and claim ceilings more visible than a scale-first perturbation atlas.", "current_gap": "No flagship NMD perturbation dataset currently connects a public Dataset Card to measured outcomes, model runs and follow-up studies.", "adoption_state": "DATA_PRODUCT_PATTERN_ADOPT_NOW_SCALE_NOT_INHERITED", "sources": [ { "title": "Tahoe platform", "url": "https://www.tahoebio.ai/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Open sourcing Tahoe-100M", "url": "https://www.tahoebio.ai/news/open-sourcing-tahoe-100m", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "Virtual-cell model builders and drug discovery teams", "entry_task": "Access a large chemical perturbation atlas", "moat": "PROPRIETARY_DATA_ENGINE_WITH_OPEN_RELEASES", "openness": "MIXED", "wet_lab_loop": "YES", "disease_specificity": "CANCER_FIRST", "evidence_transparency": "MEDIUM", "adoption_priority": "P1", "practice_not_to_copy": "Do not use cell-count scale as a substitute for donor, disease and perturbation relevance.", "local_equivalent": [ "Measured DMD evidence release", "Dataset cards" ] }, { "reference_id": "LANDSCAPE-XAIRA-XCELL", "platform": "Xaira Therapeutics · X-Cell", "category": "CAUSAL_PERTURBATION_MODEL", "observed_capability": "Packages a virtual-cell release around a named model, a large perturbation training asset, a technical report and a cross-context prediction task.", "practice_to_adopt": "Give each locally evaluated model a permanent release page that binds model version, training context, target context, artifacts, benchmark results and limitations.", "nmd_vcell_advantage": "NMD-VCell publishes negative runs, abstentions and disease-specific transfer boundaries instead of relying on a broad model launch claim.", "current_gap": "Model releases are audited, but the public product does not yet present every ModelRun as one linked release package with quickstart and failure analysis.", "adoption_state": "MODEL_RELEASE_CONTRACT_ADOPT_PERFORMANCE_NOT_INHERITED", "sources": [ { "title": "X-Cell announcement", "url": "https://www.xaira.com/news/announcing-x-cell-our-virtual-cell-model-trained-on-billions-of-genomic-data-points", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "X-Cell technical report", "url": "https://www.cdn.xaira.com/papers/X_CELL_V1_0316_final.pdf", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "AI drug discovery researchers", "entry_task": "Evaluate or apply a cross-context perturbation model", "moat": "PROPRIETARY_PERTURBATION_DATA_AND_MODEL", "openness": "MIXED", "wet_lab_loop": "YES", "disease_specificity": "GENERAL_CELL_CONTEXTS", "evidence_transparency": "MEDIUM", "adoption_priority": "P1", "practice_not_to_copy": "Do not claim cross-context DMD generalization without prospective disease-relevant validation.", "local_equivalent": [ "Model card audit", "ModelRun release objects" ] }, { "reference_id": "LANDSCAPE-RECURSION-OS", "platform": "Recursion OS · Predict–Explain–Discover", "category": "LAB_IN_THE_LOOP_DRUG_DISCOVERY", "observed_capability": "Connects automated perturbation experiments, phenomics and transcriptomics, learned maps, design workflows and downstream therapeutic programs in a physical-to-digital feedback loop.", "practice_to_adopt": "Show the complete lifecycle from experimental material through assay, data object, model, decision, new experiment and evidence update.", "nmd_vcell_advantage": "NMD-VCell can expose each evidence transition and missing link publicly even without proprietary lab scale or a drug pipeline.", "current_gap": "Study Cards and an outcome registry exist, but no measured candidate-level DMD outcome has yet completed the loop.", "adoption_state": "CLOSED_LOOP_SCHEMA_ADOPTED_MEASURED_RETURN_PENDING", "sources": [ { "title": "Recursion OS", "url": "https://www.recursion.com/platform", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "Virtual Cells: Predict, Explain, Discover", "url": "https://arxiv.org/abs/2505.14613", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "Drug discovery programs", "entry_task": "Move from perturbation maps to a therapeutic program", "moat": "AUTOMATED_LAB_DATA_MODEL_LOOP", "openness": "PROPRIETARY", "wet_lab_loop": "YES", "disease_specificity": "THERAPEUTIC_PROGRAMS", "evidence_transparency": "MEDIUM", "adoption_priority": "P0", "practice_not_to_copy": "Do not imply an automated wet-lab or therapeutic pipeline that NMD-VCell does not operate.", "local_equivalent": [ "Evidence-to-experiment loop", "Study Cards", "Outcome registry" ] }, { "reference_id": "LANDSCAPE-GENBIO-AIDO", "platform": "GenBio AI · AIDO", "category": "MULTISCALE_WORLD_MODEL", "observed_capability": "Frames DNA, RNA, protein, structure and single-cell models as interoperable modules on a roadmap toward a multiscale biological world model.", "practice_to_adopt": "Publish a layered capability roadmap that distinguishes released modules, interfaces between scales and future simulation goals.", "nmd_vcell_advantage": "NMD-VCell can make every currently supported scale and unsupported transition explicit rather than presenting a universal world-model claim.", "current_gap": "Gene, pathway, cell-state and experiment objects are linked conceptually but do not yet share one typed cross-scale relation contract.", "adoption_state": "ROADMAP_PATTERN_ADOPT_UNIVERSAL_CLAIM_REJECTED", "sources": [ { "title": "GenBio AI AIDO", "url": "https://genbio.ai/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" }, { "title": "A World Model of the Virtual Cell", "url": "https://genbio.ai/world-model-of-the-virtual-cell/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "Multiscale biological AI researchers", "entry_task": "Use or combine biological foundation models", "moat": "MULTISCALE_MODEL_SYSTEM", "openness": "MIXED", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "LOW_TO_MEDIUM", "adoption_priority": "P2", "practice_not_to_copy": "Do not use world-model language where only bounded evidence objects are available.", "local_equivalent": [ "Meaning map", "Capability atlas" ] }, { "reference_id": "LANDSCAPE-CELLULAR-INTELLIGENCE", "platform": "Cellular Intelligence", "category": "TEMPORAL_SIGNALING_ACTIVE_LEARNING", "observed_capability": "Emphasizes sequential signaling, dose, temporal order, cell-fate control and active learning over static cell-state representation.", "practice_to_adopt": "Represent intervention sequence, dose and time as first-class variables, then prioritize experiments by the uncertainty they can resolve.", "nmd_vcell_advantage": "The DMD process map and Study Cards can connect temporal signaling hypotheses to source-linked disease evidence and explicit outcome branches.", "current_gap": "Current studies record time and endpoint, but the planner does not yet compare sequential interventions or information gain across an experiment portfolio.", "adoption_state": "TEMPORAL_CONTRACT_NEXT_ACTIVE_LEARNING_FUTURE", "sources": [ { "title": "Cellular Intelligence virtual cell-signaling model", "url": "https://www.cellularintelligence.com/news/somite-becomes-cellular-intelligence", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "DIRECT", "primary_user": "Regenerative medicine and cell engineering teams", "entry_task": "Design temporal signaling interventions", "moat": "SEQUENTIAL_SIGNALING_DATA_ENGINE", "openness": "PROPRIETARY", "wet_lab_loop": "YES", "disease_specificity": "CELL_FATE", "evidence_transparency": "LOW_TO_MEDIUM", "adoption_priority": "P1", "practice_not_to_copy": "Do not inherit company-reported scale or efficiency claims as validated evidence.", "local_equivalent": [ "DMD process map", "Experiment Planner" ] }, { "reference_id": "LANDSCAPE-CELLARIUM", "platform": "Broad Cellarium AI", "category": "SINGLE_CELL_DATAOPS_MLOPS", "observed_capability": "Presents annotation, denoising, perturbation interpretation and cloud infrastructure as separate tools with task-specific identities.", "practice_to_adopt": "Turn existing NMD-VCell pages into a tool catalog only when each module has declared inputs, outputs, failure states, examples and machine interfaces.", "nmd_vcell_advantage": "NMD-VCell can bind each tool output to disease evidence, a claim ceiling and the next experiment instead of ending at a generic analysis artifact.", "current_gap": "Resolver, comparator, process inspector, model auditor and planner exist but do not yet share a visible tool contract.", "adoption_state": "TOOL_CATALOG_CONTRACT_IMPLEMENT_THIS_BUILD", "sources": [ { "title": "Cellarium AI tools", "url": "https://www.cellarium.ai/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "INFRASTRUCTURE", "primary_user": "Single-cell computational teams", "entry_task": "Run a task-specific single-cell tool", "moat": "DATAOPS_MLOPS_AND_TOOLING", "openness": "OPEN_RESEARCH", "wet_lab_loop": "NO", "disease_specificity": "GENERAL_BIOLOGY", "evidence_transparency": "HIGH", "adoption_priority": "P0", "practice_not_to_copy": "Do not label an informational page as a tool without executable inputs and outputs.", "local_equivalent": [ "Resolver", "Compare", "Process inspector", "Model auditor", "Planner" ] }, { "reference_id": "LANDSCAPE-NVIDIA-BIONEMO", "platform": "NVIDIA BioNeMo", "category": "MODEL_DEPLOYMENT_INFRASTRUCTURE", "observed_capability": "Packages biomolecular AI capabilities as frameworks, web interfaces, APIs and deployable inference microservices.", "practice_to_adopt": "Keep one model identity across web documentation, API records, local adapters, artifacts and deployment-specific run receipts.", "nmd_vcell_advantage": "NMD-VCell can provide stronger disease-specific evidence governance around externally executed or locally adapted models.", "current_gap": "The public API exposes ModelRuns, but there is no uniform adapter package or deployment receipt across external model families.", "adoption_state": "PACKAGING_CONTRACT_NEXT_INFRASTRUCTURE_NOT_REQUIRED", "sources": [ { "title": "NVIDIA BioNeMo", "url": "https://www.nvidia.com/en-us/clara/bionemo/", "source_class": "OFFICIAL_OR_PRIMARY_SOURCE", "checked_at": "2026-08-16" } ], "competitor_type": "INFRASTRUCTURE", "primary_user": "AI developers and enterprise research teams", "entry_task": "Build, adapt or deploy a biology model", "moat": "COMPUTE_PACKAGING_AND_DEPLOYMENT", "openness": "MIXED", "wet_lab_loop": "NO", "disease_specificity": "DRUG_DISCOVERY", "evidence_transparency": "MEDIUM", "adoption_priority": "P1", "practice_not_to_copy": "Do not build enterprise infrastructure before a reproducible disease adapter is needed.", "local_equivalent": [ "API", "Model adapters", "Run receipts" ] } ], "nmd_vcell_position": "Compete on neuromuscular disease specificity, source-to-decision traceability, baseline-first model audits and prospective evidence governance—not on unsupported scale parity.", "claim_boundary": "This registry is not a universal product ranking and does not imply parity, endorsement or local model validation." }, "product_contract_registry": { "registry_schema": "nmd-vcell-product-contract-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "contract_count": 4, "flagship_count": 4, "contracts": [ { "contract_id": "PRODUCT-CONTRACT-DATASET-CARD-1.0", "label": "Dataset Card", "product_role": "Turn a stored matrix or source accession into a citable, task-qualified biological data object.", "primary_question": "What was measured, in which biological units, and what can this dataset validly support?", "required_sections": [ "Identity and version", "Disease, tissue, cell state and perturbation context", "Sample, donor and statistical-unit design", "Matrix, feature, metadata and checksum inventory", "Access, licence and source provenance", "Readiness, permitted use and prohibited use", "Linked ModelRuns, benchmarks and studies" ], "required_links": [ "source record", "download or access object", "readiness gate", "downstream run or study" ], "current_route": "/resource/datasets/", "current_state": "RELEASED_PARTIAL_STANDARDIZATION", "next_gate": "Render the same required sections for every dataset and reject model-ready status when donor, feature or perturbation identity is unresolved.", "inspired_by": [ "CELLxGENE", "Tahoe-100M", "DepMap" ], "claim_boundary": "Dataset scale or availability does not establish independent biological replication or task suitability." }, { "contract_id": "PRODUCT-CONTRACT-MODEL-CARD-1.0", "label": "Model Card", "product_role": "Bind a model identity to one task, one execution history and one bounded claim surface.", "primary_question": "What did this exact model version receive, return, beat or fail, and where must it abstain?", "required_sections": [ "Model identity, version and provider", "Task, input and output object", "Training and evaluation context", "Split, leakage and baseline controls", "Metrics, seeds and local execution result", "Failure, abstention and prohibited claims", "Artifacts, run receipts and reproducibility links" ], "required_links": [ "ModelRun", "dataset digest", "benchmark task", "artifact or source", "failure analysis" ], "current_route": "/resource/models/", "current_state": "RELEASED_AUDITED", "next_gate": "Expose a uniform adapter and quickstart only after the same model identity is reproducible across documentation, API and run receipts.", "inspired_by": [ "CZI Virtual Cells Platform", "X-Cell", "NVIDIA BioNeMo" ], "claim_boundary": "Architecture reputation and external performance are not local NMD or DMD validation." }, { "contract_id": "PRODUCT-CONTRACT-BENCHMARK-CARD-1.0", "label": "Benchmark Card", "product_role": "Make model evaluation a frozen scientific task rather than a movable leaderboard claim.", "primary_question": "On which sealed outcomes, split, baselines and metrics did a model advance or stop?", "required_sections": [ "Scientific question and task identifier", "Frozen data, target context and outcome object", "Split, leakage groups and hidden-label policy", "Permanent simple baselines", "Metric families, seeds and uncertainty", "Advance or no-advance decision gate", "Immutable result and negative-run history" ], "required_links": [ "benchmark schema", "split manifest", "baseline runs", "ModelRuns", "result download" ], "current_route": "/resource/benchmarks", "current_state": "RELEASED_TASK_BOUNDED", "next_gate": "Add external adapters only on compatible frozen tasks and retain every stopped or negative result.", "inspired_by": [ "Arc Virtual Cell Challenge", "CZI Virtual Cells benchmarks" ], "claim_boundary": "A same-assay benchmark result cannot be transferred to DMD muscle or a different output distribution." }, { "contract_id": "PRODUCT-CONTRACT-WORKFLOW-OUTCOME-CARD-1.0", "label": "Workflow / Outcome Card", "product_role": "Connect a biological question to a frozen experiment, returned outcome and explicit evidence update.", "primary_question": "What experiment can change the conclusion, and how will every positive, null, toxic or failed outcome return?", "required_sections": [ "Question, estimand and hypothesis", "Intervention, cell context, dose, time and comparator", "Biological unit, controls, endpoints and QC", "Lifecycle, preregistration and immutable decision rule", "Prediction freeze when applicable", "Measured outcome, provenance and failure state", "Evidence transition and claim update" ], "required_links": [ "Study Card", "Prediction Card when applicable", "Outcome object", "source evidence", "release update" ], "current_route": "/resource/planner", "current_state": "SCHEMA_RELEASED_OUTCOME_REGISTRY_EMPTY", "next_gate": "Register one immutable DMD study and return its outcome through the same identifiers without suppressing null, toxic or failed branches.", "inspired_by": [ "Recursion OS", "Cellular Intelligence", "VCell" ], "claim_boundary": "A study design is prospective infrastructure, not a measured intervention effect." } ], "flagship_modules": [ { "module_id": "FLAGSHIP-EVIDENCE-ATLAS", "title": "Evidence Atlas", "audience": "Biologists and translational researchers", "question": "What is known in this disease, cell state and biological process?", "inputs": [ "disease", "cell context", "gene or process", "source evidence" ], "outputs": [ "source-linked evidence", "conflicts", "missing layers", "claim ceiling" ], "primary_route": "/resource/diseases/", "supporting_routes": [ "/resource/process/", "/resource/cell-browser/", "/resource/data-universe/" ], "current_outcome": "Four disease modules and donor-aware context objects are visible; evidence depth differs by disease.", "status": "RELEASED_EVIDENCE_BOUNDARY" }, { "module_id": "FLAGSHIP-VIRTUAL-CELL-MODELS", "title": "Virtual Cell Models", "audience": "Computational biologists and model developers", "question": "Can this exact task be computed, and what did each registered model actually do?", "inputs": [ "task-qualified dataset", "frozen split", "model version", "baseline contract" ], "outputs": [ "ModelRun", "benchmark decision", "failure analysis", "abstention" ], "primary_route": "/resource/models/", "supporting_routes": [ "/resource/benchmarks", "/resource/prediction_readiness", "/resource/virtual-cell/" ], "current_outcome": "Six frozen runs are registered; no calibrated candidate-level DMD model is released.", "status": "RELEASED_LIMITED_NO_DMD_PREDICTOR" }, { "module_id": "FLAGSHIP-EXPERIMENT-ENGINE", "title": "Experiment Engine", "audience": "Experimental teams and collaborators", "question": "Which controlled experiment would close the decision-critical evidence gap?", "inputs": [ "missing edge", "estimand", "cell system", "controls and endpoints" ], "outputs": [ "Study Card", "frozen decision rule", "QC plan", "return path" ], "primary_route": "/resource/planner", "supporting_routes": [ "/resource/decisions/", "/resource/study-card/ZNF133", "/resource/contribute/" ], "current_outcome": "Prospective Study Cards are available; they remain designs until registered and run.", "status": "RELEASED_DESIGN_LAYER" }, { "module_id": "FLAGSHIP-OUTCOME-REGISTRY", "title": "Outcome Registry", "audience": "Study owners, reviewers and downstream modelers", "question": "What was registered, measured, failed or released—and what conclusion changed?", "inputs": [ "registered study", "frozen prediction if applicable", "measured outcome", "provenance" ], "outputs": [ "Outcome object", "evidence transition", "updated claim boundary", "future benchmark outcome" ], "primary_route": "/resource/registry", "supporting_routes": [ "/resource/release", "/resource/api/v1.1/prospective_lifecycle.json" ], "current_outcome": "The lifecycle and schemas are public; qualifying candidate-level DMD outcomes remain 0/21.", "status": "RELEASED_EMPTY_BY_DESIGN" } ], "operating_rule": "Every public asset must resolve to a typed card, every card must name its claim boundary and next gate, and every experiment-capable path must return through the outcome registry.", "claim_boundary": "These contracts standardize presentation, provenance and decisions. They do not create missing measurements, model performance or biological validation." }, "model_opportunity_registry": { "registry_schema": "nmd-vcell-model-opportunity-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "record_count": 12, "status_vocabulary": [ "EXECUTED_LOCAL_LIMITED_PASS", "EXECUTED_LOCAL_GATE_FAIL", "EXECUTED_LOCAL_NO_GO", "EXECUTED_LOCAL_GATE_FAIL", "EXECUTED_8_LEGACY_CONFIGS_ALL_GATE_FAIL", "LOCAL_NVME_CORE_SMOKE_PASS_NO_COMPATIBLE_CHECKPOINT", "SOURCE_PINNED_INPUT_CONTRACT_FAIL", "NOT_ELIGIBLE_FOR_EXECUTION", "SOURCE_VERIFIED_NOT_RUN", "SOURCE_VERIFIED_REPRESENTATION_ONLY", "SOURCE_VERIFIED_CONTEXT_MISMATCH", "SOURCE_VERIFIED_EVALUATION_CANDIDATE" ], "records": [ { "model_id": "NMDVCELL-RIDGE-SAFE-2.3", "model_name": "Same-context ridge residual baseline", "provider": "NMD-VCell", "artifact_type": "MODEL", "model_class": "LINEAR_BASELINE", "task": "Same-context perturbation-response prediction", "context": "Processed HepG2 CRISPRi substrate", "status": "EXECUTED_LOCAL_LIMITED_PASS", "local_result": "Small mean-RMSE improvement over train mean; raw direction unsupported.", "recommended_role": "Permanent comparator on every compatible frozen task.", "next_gate": "Retain without expanding beyond the same-assay scope.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-ridge-safe-2-3-g0-repeated-fold.json" }, { "model_id": "EXTERNAL-GEARS-0.1.2", "model_name": "GEARS", "provider": "External model · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "GRAPH_PERTURBATION_MODEL", "task": "Genetic perturbation response", "context": "Five frozen HepG2 same-coverage splits", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "0/5 splits advanced; ridge won all five same-coverage comparisons.", "recommended_role": "Official negative control.", "next_gate": "No rerun without a new preregistration, data view or untouched test set.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-gears-0-1-2-five-seed-20260713.json" }, { "model_id": "EXTERNAL-SCGPT-0.2.5", "model_name": "scGPT", "provider": "Bowang Lab · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "SINGLE_CELL_FOUNDATION_MODEL", "task": "Checkpoint-supported genetic perturbation response", "context": "Restricted gene coverage on five frozen HepG2 splits", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "0/5 splits advanced; higher RMSE than same-coverage ridge.", "recommended_role": "Foundation-model negative control with coverage visible.", "next_gate": "Only reassess with a frozen adapter contract and untouched compatible task.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41592-024-02201-0" }, { "model_id": "EXTERNAL-TXPERT-CONFIG-GAT", "model_name": "TxPert public-STRING config-gat", "provider": "Recursion / Valence Labs · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "KNOWLEDGE_GRAPH_PERTURBATION_MODEL", "task": "Out-of-distribution transcriptomic perturbation response", "context": "Frozen HepG2 advancement gate", "status": "EXECUTED_LOCAL_GATE_FAIL", "local_result": "Median delta cosine 0.346196 was below train mean 0.373307.", "recommended_role": "Stopped advanced comparator.", "next_gate": "Remaining seeds stay locked unless a new prospective protocol is frozen.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41587-026-03113-4" }, { "model_id": "EXTERNAL-MORPH-1AD06D4", "model_name": "MORPH DepMap validation pilot", "provider": "External model · local NMD-VCell run", "artifact_type": "MODEL", "model_class": "GENE_EMBEDDING_PERTURBATION_MODEL", "task": "Validation-only perturbation pilot", "context": "HepG2 with DepMap Public 25Q3 embeddings", "status": "EXECUTED_LOCAL_NO_GO", "local_result": "Engineering passed; the model did not beat train mean.", "recommended_role": "Sealed negative control.", "next_gate": "Keep the v27 test partition sealed; revisions need a fresh contract.", "dmd_claim_allowed": false, "source_url": "/resource/api/v1.1/model-runs/mrun-morph-depmap25q3-validation-20260722.json" }, { "model_id": "ARC-STATE-1.0", "model_name": "STATE 1.0", "provider": "Arc Institute", "artifact_type": "MODEL", "model_class": "SET_BASED_STATE_TRANSITION_MODEL", "task": "Population-level perturbation response across contexts", "context": "Large public observational and perturbational corpora", "status": "EXECUTED_8_LEGACY_CONFIGS_ALL_GATE_FAIL", "local_result": "Eight CPU/GPU and held-out/seen-perturbation receipts were migrated; none beat both zero and train mean on every split.", "recommended_role": "Stopped comparator unless a materially new preregistered task or untouched outcome exists.", "next_gate": "Do not rerun by reputation; require a corrected preregistration, untouched truth or materially different task-compatible checkpoint.", "dmd_claim_allowed": false, "source_url": "https://github.com/ArcInstitute/state" }, { "model_id": "ARC-STACK-2026", "model_name": "Stack", "provider": "Arc Institute", "artifact_type": "MODEL", "model_class": "IN_CONTEXT_SINGLE_CELL_FOUNDATION_MODEL", "task": "In-context representation and condition transfer", "context": "Reported pretraining on 149 million uniformly processed human cells", "status": "LOCAL_NVME_CORE_SMOKE_PASS_NO_COMPATIBLE_CHECKPOINT", "local_result": "After one 180-second dependency-path timeout, a bounded local-NVMe retry passed the official StateICLModelBase forward path on a V100 with finite outputs. No pretrained checkpoint or task benchmark was run.", "recommended_role": "Runtime- and checkpoint-gated context-model hypothesis generator.", "next_gate": "Identify a task-compatible pretrained genetic checkpoint and preregister an untouched benchmark before any model-performance claim.", "dmd_claim_allowed": false, "source_url": "https://arcinstitute.org/news/foundation-model-stack" }, { "model_id": "CZI-TRANSCRIPTFORMER-0.6.0", "model_name": "TranscriptFormer", "provider": "Chan Zuckerberg Initiative", "artifact_type": "MODEL", "model_class": "CROSS_SPECIES_GENERATIVE_FOUNDATION_MODEL", "task": "Cell embeddings, classification, disease-state and regulatory inference", "context": "Up to 112 million cells across 12 species", "status": "SOURCE_VERIFIED_REPRESENTATION_ONLY", "local_result": "No NMD-VCell execution; not registered as a perturbation-response model.", "recommended_role": "Cross-species and disease-context representation benchmark.", "next_gate": "Test whether embeddings improve a frozen donor- or disease-held-out task over PCA and scVI.", "dmd_claim_allowed": false, "source_url": "https://virtualcellmodels.cziscience.com/model/transcriptformer" }, { "model_id": "BIOHUB-SCLDM-CD4-0.1", "model_name": "scLDM.CD4", "provider": "CZ Biohub Chicago", "artifact_type": "MODEL", "model_class": "LATENT_FLOW_MATCHING_PERTURBATION_MODEL", "task": "Conditional perturbed profile generation", "context": "Primary human CD4+ T cells", "status": "SOURCE_VERIFIED_CONTEXT_MISMATCH", "local_result": "No NMD-VCell execution; CD4 context does not match muscle disease tasks.", "recommended_role": "Architecture reference, not a direct adapter priority.", "next_gate": "Require a compatible muscle perturbation corpus before adaptation is considered.", "dmd_claim_allowed": false, "source_url": "https://virtualcellmodels.cziscience.com/model/scldm-cd4" }, { "model_id": "CELLOT-2023", "model_name": "CellOT", "provider": "ETH Zurich and collaborators", "artifact_type": "MODEL", "model_class": "NEURAL_OPTIMAL_TRANSPORT", "task": "Distribution-to-distribution perturbation response", "context": "Unpaired treated and untreated single-cell populations", "status": "SOURCE_VERIFIED_NOT_RUN", "local_result": "No frozen NMD-VCell run.", "recommended_role": "Distribution-modeling comparator on compatible public drug/cytokine data.", "next_gate": "Compare against identity, mean-shift, linear and nearest-neighbour transport baselines on a sealed split.", "dmd_claim_allowed": false, "source_url": "https://www.nature.com/articles/s41592-023-01969-x" }, { "model_id": "CPA-2023", "model_name": "Compositional Perturbation Autoencoder", "provider": "Meta Research / scverse collaborators", "artifact_type": "MODEL", "model_class": "COMPOSITIONAL_GENERATIVE_MODEL", "task": "Dose, drug and combination response", "context": "High-throughput single-cell perturbation screens", "status": "SOURCE_VERIFIED_NOT_RUN", "local_result": "No frozen NMD-VCell run.", "recommended_role": "Permanent compositional baseline candidate for chemical tasks.", "next_gate": "Use only where dose, covariate and perturbation metadata are complete.", "dmd_claim_allowed": false, "source_url": "https://github.com/facebookresearch/CPA" }, { "model_id": "PERTURBENCH-2025", "model_name": "PerturBench", "provider": "Altos Labs and collaborators", "artifact_type": "BENCHMARK_FRAMEWORK", "model_class": "STANDARDIZED_EVALUATION", "task": "Cellular perturbation model benchmarking", "context": "Multiple datasets, model families and metric views", "status": "SOURCE_VERIFIED_EVALUATION_CANDIDATE", "local_result": "Not yet adopted as the NMD-VCell evaluation runtime.", "recommended_role": "Benchmark adapter and metric cross-check, not a predictor.", "next_gate": "Map NMD-VCell ModelRun inputs and outputs into PerturBench while preserving the existing metric firewall and simple baselines.", "dmd_claim_allowed": false, "source_url": "https://papers.nips.cc/paper_files/paper/2025/file/8aee537279a66ced96319dfca3c00002-Paper-Datasets_and_Benchmarks_Track.pdf" } ], "selection_rule": "Prefer task compatibility, complete metadata, reproducible code/checkpoints and baseline-comparable evaluation over novelty or parameter count.", "canonical_status_registry": "/resource/api/v1.1/model_execution_status_registry.json", "current_decision": "The first compatibility batch is executed without a DMD upgrade. Prioritize matched DMD intervention outcomes; rerun external models only after their explicit source, runtime, input and task gates pass.", "calibrated_dmd_model_count": 0, "claim_boundary": "Source verification means the publication, code or model card exists. It does not mean NMD-VCell reproduced the result or that the model transfers to DMD muscle." }, "data_opportunity_registry": { "registry_schema": "nmd-vcell-data-opportunity-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-16", "generated_by": "scripts/apply-evidence-atlas-product-overlay.mjs", "record_count": 13, "records": [ { "opportunity_id": "DATA-AUTHOR-MISSING-FEATURE-METADATA", "name": "Author-missing feature and metadata files", "provider": "Source authors / existing DMD perturbation study", "data_class": "DECISION_CRITICAL_SOURCE_RECOVERY", "scale": "Unknown until files are obtained", "perturbation": "Potentially disease-relevant; identity contract incomplete", "context": "DMD myoblast / source-study context under audit", "access_state": "AUTHOR_CONTACT_OR_ARCHIVE_RECOVERY_REQUIRED", "feature_metadata_state": "MISSING", "direct_dmd_candidate_outcome": false, "priority": "P0", "recommended_use": "Recover identifiers, columns, sample mapping and feature semantics before any reanalysis.", "next_action": "Request the exact feature table, sample metadata, perturbation identity mapping and processing description; checksum every returned file.", "source_url": "/resource/datasets/", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE288958-DMD-HUMAN-MUSCLE", "name": "GSE288958 human DMD/BMD/control muscle snRNA-seq and spatial context", "provider": "Jeon et al. / NCBI GEO", "data_class": "HUMAN_DMD_SINGLE_NUCLEUS_AND_SPATIAL", "scale": "11 human muscle samples: 5 control, 3 BMD and 3 DMD", "perturbation": "Disease and treatment-mechanism context; no candidate perturbation outcome", "context": "Human quadriceps/abdomen muscle biopsies with DMD, BMD and control groups", "access_state": "PUBLIC_GEO_AND_LOCAL_PROCESSED_ASSETS", "feature_metadata_state": "PUBLIC_MATRIX_AND_SAMPLE_METADATA", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Donor-resolved DMD cell-state signatures, context validation and treatment-mechanism stratification.", "next_action": "Preserve donor/sample units, harmonize cell-state labels and keep disease context separate from candidate perturbation response.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE277637-DMD-ORGANOID", "name": "GSE277637 DMD iPSC-derived skeletal-muscle organoid scRNA-seq", "provider": "Kindler et al. / NCBI GEO", "data_class": "HUMAN_DMD_ORGANOID_SINGLE_CELL", "scale": "4 10x samples: 1 healthy iPSC control and 3 DMD patient-derived iPSC lines", "perturbation": "DMD disease context; no candidate perturbation outcome", "context": "Human iPSC-derived skeletal-muscle organoids with myogenic progenitor/satellite-cell focus", "access_state": "PUBLIC_GEO_LOCAL_INGEST_AVAILABLE", "feature_metadata_state": "PUBLIC_RAW_MATRIX_WITH_SAMPLE_LABELS", "direct_dmd_candidate_outcome": false, "priority": "P1", "recommended_use": "Organoid-specific DMD/control baseline and myogenic progenitor state validation.", "next_action": "Analyze as an organoid layer with line-aware units; do not pool it with patient biopsy muscle or call it a candidate screen.", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE277637", "direct_dmd_candidate_truth": false }, { "opportunity_id": "DATA-GSE293514-HUMAN-MYOBLAST-CROPSEQ", "name": "GSE293514 human-myoblast CROP-seq fusion screen", "provider": "Bi et al. / NCBI GEO", "data_class": "HUMAN_MYOBLAST_FUNCTIONAL_CROPSEQ", "scale": "57 samples; 250-hit mini-library; 3.7 GB count matrix and 36.3 MB deposited metadata", "perturbation": "Split-pool CROP-seq with GM, DM2d and DM6d myoblast differentiation states", "context": "Human myoblast fusion and early myogenic differentiation; 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It does not grant a dataset model-ready status merely because its GEO accession is public." }, "context_objects": [ { "registry_schema": "nmd-vcell-context-object/1.0", "object_id": "CONTEXT:GSE277637:LINE_AWARE_DMD_ORGANOID:1.0", "object_type": "LINE_AWARE_DISEASE_CONTEXT", "lifecycle_status": "CITABLE_LOCAL_CONTEXT_OBJECT_NOT_PUBLIC_MATRIX_RELEASE", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-09", "dataset_id": "GSE277637", "accession": "GSE277637", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE277637", "evidence_state": "MEASURED_EXTERNAL_DMD_DISEASE_AXES_WITH_SHARED_CONTROL", "public_state": "METADATA_QC_AND_CHECKSUMS_ONLY_SOURCE_MATRIX_NOT_REHOSTED", "context_role": "DMD organoid disease-axis heterogeneity stress test", "inferential_unit": "iPSC-derived line/sample; cells are nested observations, not independent biological replicates", "design": { "samples": 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It does not support candidate perturbation response, therapeutic efficacy, clinical prediction or a calibrated DMD predictor.", "next_gate": "Freeze line-aware sample metadata, verify GEO source terms and publish the checksum/license record before considering any portable matrix release." } ], "source_recovery_registry": { "registry_schema": "nmd-vcell-source-recovery/1.0", "recovery_id": "RECOVERY:GSE293514:IDENTITY_ARTIFACTS:1.0", "object_type": "SOURCE_IDENTITY_RECOVERY_PACKAGE", "lifecycle_status": "AUTHOR_CONTACT_OR_ARCHIVE_RECOVERY_REQUIRED", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-09", "dataset_id": "GSE293514", "accession": "GSE293514", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE293514", "public_source_inventory": { "checked_at": "2026-08-09", "availability_state": "PUBLIC_MATRIX_AND_METADATA_DOWNLOADABLE_GUIDE_IDENTITY_NOT_PUBLIC", "public_files": 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conserved and guide fields are populated or explicitly marked non-targeting/unassigned." }, { "artifact_id": "guide_reference", "filename": "final_guide_reference.csv", "purpose": "Guide sequence, target identity and control definitions", "required_fields": [ "guide_id", "guide_sequence", "target_gene", "guide_type", "control_class", "positive_control_rule" ], "acceptance": "MYOD/MYMK positive-control rules, non-targeting controls and duplicate-guide rules are explicit." }, { "artifact_id": "run_mapping", "filename": "cropseq_run_barcode_mapping.csv", "purpose": "Mapping between eight guide-only runs, transcriptome sublibraries, Parse barcode keys and final bc_wells IDs", "required_fields": [ "run_id", "library_id", "parse_barcode_key", "bc_wells", "cell_barcode", "guide_barcode" ], "acceptance": "Each retained cell has one auditable path from guide run to transcriptome cell identity." }, { "artifact_id": "processed_output", "filename": "author_processed_fig6_output.h5ad", "purpose": 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"Only then assess whether any object can support healthy-myoblast context transfer; no DMD claim is implied." ], "unlocks": [ "Exact CROP-seq reanalysis decision", "Guide-resolved technical reconstruction", "A bounded healthy-myoblast muscle-context benchmark if all gates pass" ], "does_not_unlock": [ "DMD candidate perturbation truth", "Therapeutic efficacy", "Clinical prediction" ], "claim_boundary": "GSE293514 remains a healthy-myoblast screen/context object until feature identity, guide identity and processing provenance are restored. Public accession alone does not authorize expression-level transfer." }, "source_recovery_preflight": { "preflight_schema": "nmd-vcell-source-recovery-preflight/1.0", "preflight_id": "PREFLIGHT:GSE293514:IDENTITY_ARTIFACTS:1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-09", "dataset_id": "GSE293514", "candidate_root": "neuromuscular_virtual_cell/data/external/GSE293514/author_recovery", "status": "BLOCKED_MISSING_OR_INVALID_IDENTITY_ARTIFACTS", "checks": [ { "artifact_id": "all_genes", "filename": "all_genes.csv", "state": "MISSING", "path": "all_genes.csv", "size_bytes": null, "sha256": null, "missing_fields": [ "feature_index", "ensembl_id", "gene_symbol", "reference_build", "ensembl_release" ], "row_count": null, "notes": "Required author/source artifact is not present in the candidate recovery directory." }, { "artifact_id": "cell_metadata", "filename": "cell_metadata_2000_new.csv", "state": "MISSING", "path": "cell_metadata_2000_new.csv", "size_bytes": null, "sha256": null, "missing_fields": [ "barcode", "sample_2", "guide_infect", "guide3", "guide4", "guide_type", "AKAcluster", "sig_group", "sig_group2", "AKAcluster2", "human_disease" ], "row_count": null, "notes": "Required author/source artifact is not present in the candidate recovery directory." }, { "artifact_id": "guide_reference", "filename": "final_guide_reference.csv", "state": "MISSING", "path": "final_guide_reference.csv", "size_bytes": null, "sha256": null, "missing_fields": [ "guide_id", "guide_sequence", "target_gene", "guide_type", "control_class", "positive_control_rule" ], "row_count": null, "notes": "Required author/source artifact is not present in the candidate recovery directory." }, { "artifact_id": "run_mapping", "filename": "cropseq_run_barcode_mapping.csv", "state": "MISSING", "path": "cropseq_run_barcode_mapping.csv", "size_bytes": null, "sha256": null, "missing_fields": [ "run_id", "library_id", "parse_barcode_key", "bc_wells", "cell_barcode", "guide_barcode" ], "row_count": null, "notes": "Required author/source artifact is not present in the candidate recovery directory." }, { "artifact_id": "processed_output", "filename": "author_processed_fig6_output.h5ad", "state": "MISSING", "path": "author_processed_fig6_output.h5ad", "size_bytes": null, "sha256": null, "missing_fields": [ "obs", "var", "X", "uns.processing_provenance" ], "row_count": null, "notes": "Required author/source artifact is not present in the candidate recovery directory." } ], "gates": { "files_present": false, "feature_identity": false, "cell_metadata_identity": false, "guide_reference_identity": false, "guide_to_cell_mapping": false, "processing_output_present": false, "processing_output_verified": false, "author_identity_complete": false, "biological_transfer": false }, "next_action": "Place the five requested de-identified artifacts in the candidate recovery directory, then rerun this preflight.", "claim_boundary": "A passing file preflight does not create DMD candidate perturbation truth. Biological transfer remains blocked until author processing, controls and claim-specific validation are independently reproduced.", "direct_dmd_candidate_perturbation_truth": "0/21" }, "portable_import_registry": { "registry_schema": "nmd-vcell-portable-import-registry/1.0", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-09", "records": [ { "dataset_id": "GSE288958", "accession": "GSE288958", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "status": "LOCAL_AUTHORITATIVE_RDS_OPENED_IDENTIFIERS_RECONCILED_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN", "authoritative_source_state": "LOCAL_RDS_SHA256_CHECKSUMMED_OBJECT_OPENED_IDENTIFIERS_RECONCILED_MATRIX_QC_AND_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN", "external_source_reference": "EXTERNAL_SHARE_RDS:gse288958_reference_qc_umap_annotated.rds", "official_source_inventory": { "checked_at": "2026-08-09", "availability_state": "PUBLIC_RAW_ARCHIVE_FULL_TAR_VALIDATED_FEATURE_SUPPLEMENT_CHECKSUMMED", "public_files": [ { "filename": "GSE288958_RAW.tar", "file_type": "TAR_OF_MTX_TSV", "size_bytes": 359823360, "official_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE288nnn/GSE288958/suppl/GSE288958_RAW.tar", "local_state": "FULL_DOWNLOAD_TAR_VALIDATED", "local_path": "neuromuscular_virtual_cell/data/external/GSE288958/raw/GSE288958_RAW.tar", "local_size_bytes": 359823360, "local_sha256": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "tar_validation": { "member_count": 32, "matrix_members": 11, "barcode_members": 11, "feature_members": 10, "gzip_streams_passed": 32 } }, { "filename": "GSE288958_BMD_1_features.tsv.gz", "file_type": "TSV_FEATURE_TABLE", "official_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE288nnn/GSE288958/suppl/GSE288958_BMD_1_features.tsv.gz", "local_state": "LOCAL_CHECKSUMMED", "local_path": "neuromuscular_virtual_cell/data/external/GSE288958/raw/GSE288958_BMD_1_features.tsv.gz", "local_size_bytes": 333437, "local_sha256": "f99a146106e8e37a1bf5933e9ee3bc84139ffee889540ea0425fd3f9fbeef4a7", "gzip_validation": "PASS" }, { "filename": "GSE288958_family.soft.gz", "file_type": "GEO_FAMILY_SOFT_METADATA", "official_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE288nnn/GSE288958/soft/GSE288958_family.soft.gz", "local_state": "LOCAL_CHECKSUMMED", "local_path": "neuromuscular_virtual_cell/data/external/GSE288958/raw/GSE288958_family.soft.gz", "local_size_bytes": 3433, "local_sha256": "7a833abb4227d62d54c323fc16c1bc0eded7f4c8226326348b4d81e919184e3e", "gzip_validation": "PASS" } ], "source_gap": "The official processed matrix archive, BMD_1 feature supplement, GEO family SOFT metadata, raw barcode inventory, inherited coarse-label export and checksum-matched authoritative RDS are local. 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"PILOT_ARTIFACT_ONLY", "size_bytes": 1729, "sha256": "8fe018f042c9b0b6dde122a62fb300eecaef5dadb60f7cc97ed08c30c8aecc78" }, { "role": "pilot_detection_summary", "path": "GFOD2_DMD_standalone/results/server_pilot/gse288958_gfod2_detection_by_sample_celltype.tsv", "state": "PILOT_ARTIFACT_ONLY", "size_bytes": 6754, "sha256": "79e8daaeaef44473df1ae6af519e507939166e12bb2fcfd32cb530ef27ff519b" } ], "required_portable_objects": [ "authoritative source matrix or H5AD/RDS with a portable checksum", "sample metadata with donor, disease, biopsy site, age and batch", "opened cell annotation object with inherited-label provenance and an independent disagreement audit", "source software version and reference-build statement" ], "open_optional_promotion_objects": [ "unfiltered droplet matrix or author contamination estimate for ambient-RNA closure", "exact author command, sample sheet, read structure, whitelist, reference checksum and FASTQ aggregation manifest", "subject-level identity and batch metadata for future disease-effect inference", "spatial coordinates/object if any future spatial claim is retained" ], "acceptance_gates": [ "The authoritative object opens from a workspace-local path without external-share dependencies.", "Cell identifiers, sample identifiers and matrix dimensions reconcile.", "Disease, sample/biopsy unit, site and age fields are explicit; unavailable subject identity and batch remain declared.", "Independent donor-wise doublet sensitivity and marker-label disagreement audits are checksum-addressed before reuse.", "Pilot compartment selection remains descriptive and does not become a disease-effect test." ], "claim_ceiling": "Supports donor-resolved disease-state and cell-context validation only after portable import. 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"neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv" ] }, { "scope_id": "adjacent_gfod2_project", "logical_root": "24.GFOD2", "root_present": true, "file_inventory_count": 1075, "dataset_anchor_file_count": 29, "text_files_read": 10, "dataset_bound_artifact_filename_hits": [], "dataset_bound_parameter_reference_content_hits": [], "dataset_anchor_examples": [ "24.GFOD2/configs/gse288958_m01b_scrublet_plan_v1.yaml", "24.GFOD2/configs/gse288958_m01b_sensitivity_plan_v1.yaml", "24.GFOD2/configs/gse288958_validation_compartment_freeze_v1.yaml", "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "24.GFOD2/data/manifests/gse288958_donor_metadata.tsv", "24.GFOD2/data/manifests/gse288958_object_cells.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_manifest.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_sha256.tsv", "24.GFOD2/mechanism_target_reboot/phase15_restrained_submission_figures/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase16_submission_revision_20260819/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase17_submission_revision_20260824/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/reports/GSE288958_AMBIENT_AND_DOUBLET_INPUT_AUDIT.md", "24.GFOD2/runs/logs/gse288958_export_object_cells_20260720.log", "24.GFOD2/runs/logs/gse288958_m01b_sensitivity_20260720.log", "24.GFOD2/runs/logs/gse288958_milestone01_audit_20260720.log", "24.GFOD2/runs/logs/gse288958_raw_checksum_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_recovery_20260720.log", "24.GFOD2/scripts/server/03_gse288958_milestone01_audit.R", "24.GFOD2/scripts/server/04_gse288958_m01b_sensitivity.R", "24.GFOD2/scripts/server/05_export_gse288958_object_cells.R", "24.GFOD2/scripts/server/05_gse288958_scrublet_audit.py", "24.GFOD2/scripts/server/06_gse288958_scrublet_integration.R", "24.GFOD2/scripts/server/07_checksum_gse288958_raw_inputs.R", "24.GFOD2/scripts/server/21_planb_gse288958_analysis.R" ] } ], "result": { "dataset_bound_artifact_filename_hits": 4, "dataset_bound_exact_parameter_content_hits": 0, "proxy_or_audit_parameter_reference_hit_count": 4, "author_evidence_file_count": 0, "exact_author_command_found": false, "exact_sample_sheet_found": false, "exact_read_cycle_contract_found": false, "exact_barcode_whitelist_found": false, "exact_reference_package_found": false, "exact_fastq_aggregation_manifest_found": false, "conclusion": "No dataset-bound exact author Cell Ranger command, sample sheet, read-cycle contract, barcode whitelist, reference package checksum or FASTQ aggregation manifest was found in the searched local scopes. Proxy plans, audit scripts and reports are retained as references but do not count as author evidence. This is an inventory-limited negative result, not proof that the materials do not exist elsewhere." }, "non_binding_rule": "Do not transfer read structure, whitelist, reference package or command parameters from another accession or another project into GSE288958.", "next_action": "Request the six author-confirmation items listed in the processing contract before claiming author-exact raw reprocessing; they are optional for the bounded read-only processed-reference context release." } }, { "artifact_id": "author_parameter_request", "state": "PRESENT", "candidate_names": [ "../author_parameter_request/gse288958_author_parameter_request.json", "../author_parameter_request/GSE288958_author_parameter_request.json" ], "path": "../author_parameter_request/gse288958_author_parameter_request.json", "size_bytes": 9884, "sha256": "9aea6ceca6c4cd4386f3f00deaddffdab616f8bb4725d327a879979a30a7da7a", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-author-parameter-request/1.0", "request_id": "GSE288958-AUTHOR-PARAMETERS-20260810", "checked_at": "2026-08-10", "dataset": { "geo_accession": "GSE288958", "bioproject": "PRJNA1218529", "sra_study": "SRP561176", "sample_scope": 11, "reported_processing": { "assay": "single-nucleus RNA-seq from flow-cytometry-isolated nuclei", "chemistry": "10x Genomics Single Cell Chromium 3' V3 / CG000183", "sequencing": "paired-end 200 bp; Illumina NovaSeq 6000", "software": "Cell Ranger v6.0.0", "reference_family": "human GRCh38/hg38 pre-mRNA transcriptome reference provided by 10x Genomics" } }, "purpose": "Close the six reproducibility gaps before staging the 11 SRA runs and reproducing raw_feature_bc_matrix plus filtered_feature_bc_matrix.", "current_evidence": [ { "logical_path": "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "sha256": "11e68551807df06d83dbd6fce0fd4b092efb9c0d2cac3e67d0421ae0a0e73fbb", "records": 11 }, { "logical_path": "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "sha256": "fbd26d2689d8e65482e9df4d12dcf88f9921c794fa8f6939025b3eb7cd7d267b", "records": 11 }, { "logical_path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_parameter_recovery_audit.json", "status": "inventory-limited-negative", "exact_parameter_material_hits": 0 } ], "current_contract": { "logical_path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_processing_contract.json", "status": "PARTIAL_PROCESSING_CONTRACT_AUTHOR_CONFIRMATION_REQUIRED", "source_method_evidence_present": true, "processing_contract_complete": false, "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false }, "request_items": [ { "item_id": "AP-01", "priority": "P0", "title": "Original Cell Ranger command, sample sheet and aggregation settings", "request": "Provide the exact command line, sample sheet or command export used for all 11 samples, including count/aggr/multi mode and any aggregation step.", "required_fields": [ "cellranger_version", "mode", "command_or_sample_sheet", "fastqs_argument_or_library_input", "transcriptome_argument", "chemistry_argument_or_auto_detection", "expect_cells_or_force_cells_if_set", "include_introns_if_set", "create_bam_if_set", "localcores_and_localmem_if_recorded", "aggregation_parameters_if_used" ], "acceptable_evidence": [ "original shell command or scheduler script", "original Cell Ranger sample sheet or multi config CSV", "author-confirmed plain-text reconstruction with explicit unknown fields" ], "not_sufficient": [ "SOFT processing prose alone", "default Cell Ranger command inferred by the analyst" ], "response_status": "PENDING" }, { "item_id": "AP-02", "priority": "P0", "title": "R1/i7/i5/R2 read-cycle allocation", "request": "Provide the actual sequencing cycle allocation and index orientation for the paired-end libraries.", "required_fields": [ "layout", "r1_cycles", "i7_cycles", "i5_cycles", "r2_cycles", "index_orientation", "instrument_run_or_flowcell_if_available" ], "acceptable_evidence": [ "BCL/FASTQ run sheet", "sequencer sample sheet", "author-confirmed cycle table" ], "not_sufficient": [ "paired-end 200 bp without per-read allocation", "generic 10x V3 specification" ], "response_status": "PENDING" }, { "item_id": "AP-03", "priority": "P0", "title": "10x barcode whitelist and chemistry detection", "request": "Provide the exact barcode whitelist name/version and whether Cell Ranger chemistry auto-detection was used.", "required_fields": [ "whitelist_name", "whitelist_version_or_release", "whitelist_file_or_package_path_if_available", "chemistry_auto_detected", "barcode_read_and_orientation" ], "acceptable_evidence": [ "Cell Ranger log", "reference/package manifest", "author-confirmed whitelist record" ], "not_sufficient": [ "assume the default 10x V3 whitelist", "barcode list recovered from a different accession" ], "response_status": "PENDING" }, { "item_id": "AP-04", "priority": "P0", "title": "Exact 10x GRCh38/hg38 pre-mRNA reference package", "request": "Provide the exact reference package identifier, release/version, build date and checksum used for Cell Ranger.", "required_fields": [ "package_id", "package_version_or_release_date", "assembly", "pre_mrna_or_intronic_policy", "reference_sha256", "fasta_gtf_or_package_manifest_if_available" ], "acceptable_evidence": [ "10x reference package manifest", "Cell Ranger reference directory checksum manifest", "author-confirmed package record" ], "not_sufficient": [ "GRCh38/hg38 family label without package identity", "a current 10x reference substituted for the historical package" ], "response_status": "PENDING" }, { "item_id": "AP-05", "priority": "P1", "title": "Feature-reference CSV usage", "request": "Confirm whether a Cell Ranger feature-reference CSV was supplied; if yes, provide the file and checksum, and if no, explicitly record none.", "required_fields": [ "feature_reference_used", "feature_reference_filename_if_used", "feature_reference_sha256_if_used", "feature_reference_columns_if_used", "explicit_none_confirmation_if_not_used" ], "acceptable_evidence": [ "original Cell Ranger command/config", "feature-reference CSV", "author-confirmed none/used statement" ], "not_sufficient": [ "public gene feature table treated as a feature-reference CSV", "assumption based on assay name" ], "response_status": "PENDING" }, { "item_id": "AP-06", "priority": "P0", "title": "FASTQ naming, lane/run aggregation and library IDs", "request": "Provide the mapping from the 11 GSM/sample units to SRA run IDs, library IDs, flowcell/lane information and FASTQ filename patterns.", "required_fields": [ "sample_or_gsm", "sra_run_or_original_run_id", "library_id", "flowcell_and_lane_if_available", "fastq_filename_pattern", "lane_aggregation_rule", "sample_sheet_sample_id_or_library_id" ], "acceptable_evidence": [ "FASTQ manifest", "sample sheet", "sequencing core delivery manifest", "author-confirmed mapping table" ], "not_sufficient": [ "SRA RunInfo alone", "analyst-created filename convention without author confirmation" ], "response_status": "PENDING" } ], "run_scope": [ { "sample_name": "BMD_1", "gsm": "GSM8779832", "run": "SRR32206096", "disease": "BMD" }, { "sample_name": "BMD_2", "gsm": "GSM8779833", "run": "SRR32206095", "disease": "BMD" }, { "sample_name": "BMD_3", "gsm": "GSM8779834", "run": "SRR32206094", "disease": "BMD" }, { "sample_name": "DMD1", "gsm": "GSM8779835", "run": "SRR32206093", "disease": "DMD" }, { "sample_name": "DMD2", "gsm": "GSM8779836", "run": "SRR32206092", "disease": "DMD" }, { "sample_name": "DMD_3", "gsm": "GSM8779837", "run": "SRR32206100", "disease": "DMD" }, { "sample_name": "Normal1", "gsm": "GSM8779827", "run": "SRR32206102", "disease": "control" }, { "sample_name": "Normal_2", "gsm": "GSM8779828", "run": "SRR32206101", "disease": "control" }, { "sample_name": "Normal_3", "gsm": "GSM8779829", "run": "SRR32206099", "disease": "control" }, { "sample_name": "Normal_4", "gsm": "GSM8779830", "run": "SRR32206098", "disease": "control" }, { "sample_name": "Normal_5", "gsm": "GSM8779831", "run": "SRR32206097", "disease": "control" } ], "response_format": { "preferred": "Fill gse288958_author_parameter_response.template.json or return equivalent JSON/Markdown with one response per item_id.", "required_provenance": [ "provider or author", "date", "source filename or statement", "whether exact/original or reconstructed", "checksum for every returned file" ], "unknown_field_rule": "Use UNKNOWN_AUTHOR_NOT_RECORDED when the field cannot be recovered; do not silently fill a default.", "signed_confirmation_rule": "If an original file is unavailable, the author should explicitly confirm which fields are known, reconstructed or unavailable." }, "validation_sequence": [ "Checksum every returned file and bind it to the response item.", "Rebuild gse288958_processing_contract.json with the returned values and source paths.", "Check that all P0 items are exact or author-confirmed; retain explicit unknowns.", "Only after contract completion, stage the 11 SRA runs and record per-run checksums.", "Generate raw_feature_bc_matrix and filtered_feature_bc_matrix, then reconcile sample/cell/feature identities before formal QC." ], "prohibited_substitutes": [ "Parameters from another accession or another project", "Default 10x/Cell Ranger settings not confirmed for this dataset", "Published method prose used as a substitute for exact read cycles or package checksum", "Filtered matrix, proxy annotation or Scrublet sensitivity as a substitute for raw processing provenance" ], "claim_boundary": "This package requests missing reproducibility evidence. It does not authorize SRA download, raw reprocessing, formal QC, disease-effect testing or DMD candidate transfer. Direct DMD candidate perturbation truth remains 0/21." } }, { "artifact_id": "processing_contract", "state": "PRESENT", "candidate_names": [ "../metadata/gse288958_processing_contract.json", "../metadata/GSE288958_processing_contract.json" ], "path": "../metadata/gse288958_processing_contract.json", "size_bytes": 32794, "sha256": "e90a5f3dccb2e46969e2d30f183181244d9094a06efc56ed8d67ae803f152a7f", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-processing-contract/1.0", "dataset_id": "GSE288958", "checked_at": "2026-09-09", "status": "PARTIAL_PROCESSING_CONTRACT_AUTHOR_CONFIRMATION_REQUIRED", "source_scope": { "geo_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "bioproject": "PRJNA1218529", "sra_study": "SRP561176", "sample_scope": 11, "disease_scope": { "control": 5, "bmd": 3, "dmd": 3 } }, "evidence": { "geo_sample_soft": { "path": "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "sha256": "11e68551807df06d83dbd6fce0fd4b092efb9c0d2cac3e67d0421ae0a0e73fbb", "sample_records": 11 }, "sra_runinfo": { "path": "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "sha256": "fbd26d2689d8e65482e9df4d12dcf88f9921c794fa8f6939025b3eb7cd7d267b", "run_records": 11 } }, "parameter_recovery_search": { "manifest_schema": "nmd-vcell-gse288958-parameter-recovery-audit/1.0", "dataset_id": "GSE288958", "checked_at": "2026-09-09", "audit_scope": "local workspace project plus adjacent GFOD2 project inventory", "search_policy": { "dataset_anchors": [ "GSE288958", "PRJNA1218529", "SRP561176" ], "filename_artifacts": [ "cellranger_command", "sample_sheet", "fastq_manifest", "barcode_whitelist", "read_cycle", "reference_package" ], "exact_content_artifacts": [ "cellranger_command", "sample_sheet", "read_cycle", "barcode_whitelist", "reference_package", "fastq_manifest" ], "excluded_binary_or_generated_content": [ "RDS/H5/H5AD/TAR/GZIP/ZIP/PDF/image files", "generated public/Next build directories", "this audit, processing contract and P15/P16 reports" ] }, "scopes": [ { "scope_id": "current_project", "logical_root": "neuromuscular_virtual_cell", "root_present": true, "file_inventory_count": 15366, "dataset_anchor_file_count": 107, "text_files_read": 29, "dataset_bound_artifact_filename_hits": [ { "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/fastq_layout_preflight/SRR32206102/fasterq_output_10x_v3_whitelist_validation.json", "artifact_ids": [ "barcode_whitelist" ] }, { "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/fastq_layout_preflight/SRR32206102/sra_spot_10x_v3_whitelist_validation.json", "artifact_ids": [ "barcode_whitelist" ] }, { "path": "neuromuscular_virtual_cell/reports/P20_GSE288958_FASTQ_LAYOUT_PREFLIGHT_20260811.md", "artifact_ids": [ "fastq_manifest" ] }, { "path": "neuromuscular_virtual_cell/reports/P22_GSE288958_CELLRANGER_SUBSET_PREFLIGHT_20260811.md", "artifact_ids": [ "cellranger_command" ] } ], "dataset_bound_parameter_reference_content_hits": [ { "path": "neuromuscular_virtual_cell/reports/P18_GSE288958_REMOTE_RAW_EXECUTION_IN_PROGRESS_20260810.md", "artifact_ids": [ "read_cycle", "barcode_whitelist", "reference_package", "fastq_manifest" ] }, { "path": "neuromuscular_virtual_cell/reports/P19_GSE288958_DOWNSTREAM_PREFLIGHT_20260811.md", "artifact_ids": [ "cellranger_command", "sample_sheet", "barcode_whitelist", "reference_package" ] }, { "path": "neuromuscular_virtual_cell/reports/P20_GSE288958_FASTQ_LAYOUT_PREFLIGHT_20260811.md", "artifact_ids": [ "sample_sheet", "read_cycle", "barcode_whitelist", "reference_package" ] }, { "path": "neuromuscular_virtual_cell/reports/P22_GSE288958_CELLRANGER_SUBSET_PREFLIGHT_20260811.md", "artifact_ids": [ "barcode_whitelist" ] } ], "dataset_anchor_examples": [ 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"neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_overlay/gse288958_candidate_context_overlay.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_overlay/gse288958_candidate_context_overlay.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_triage/gse288958_candidate_context_triage.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_context_triage/gse288958_candidate_context_triage.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_guide_reference_coverage/gse288958_candidate_guide_reference_coverage.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_guide_reference_coverage/gse288958_candidate_guide_reference_coverage.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_validation_queue/gse288958_candidate_validation_queue.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/candidate_validation_queue/gse288958_candidate_validation_queue.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.md", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_sample.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_celltype_counts_by_sample.tsv", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_preflight.json", "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv" ] }, { "scope_id": "adjacent_gfod2_project", "logical_root": "24.GFOD2", "root_present": true, "file_inventory_count": 1075, "dataset_anchor_file_count": 29, "text_files_read": 10, "dataset_bound_artifact_filename_hits": [], "dataset_bound_parameter_reference_content_hits": [], "dataset_anchor_examples": [ "24.GFOD2/configs/gse288958_m01b_scrublet_plan_v1.yaml", "24.GFOD2/configs/gse288958_m01b_sensitivity_plan_v1.yaml", "24.GFOD2/configs/gse288958_validation_compartment_freeze_v1.yaml", "24.GFOD2/data/manifests/GSE288958_GEO_samples_full_20260720.soft", "24.GFOD2/data/manifests/GSE288958_PRJNA1218529_RunInfo_20260720.csv", "24.GFOD2/data/manifests/gse288958_donor_metadata.tsv", "24.GFOD2/data/manifests/gse288958_object_cells.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_manifest.tsv", "24.GFOD2/data/manifests/gse288958_raw_matrix_sha256.tsv", "24.GFOD2/mechanism_target_reboot/phase15_restrained_submission_figures/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase16_submission_revision_20260819/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/mechanism_target_reboot/phase17_submission_revision_20260824/source_data/Figure_2/gse288958_edgeR_all_tested_genes.tsv", "24.GFOD2/reports/GSE288958_AMBIENT_AND_DOUBLET_INPUT_AUDIT.md", "24.GFOD2/runs/logs/gse288958_export_object_cells_20260720.log", "24.GFOD2/runs/logs/gse288958_m01b_sensitivity_20260720.log", "24.GFOD2/runs/logs/gse288958_milestone01_audit_20260720.log", "24.GFOD2/runs/logs/gse288958_raw_checksum_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_integration_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_20260720.log", "24.GFOD2/runs/logs/gse288958_scrublet_isolated_recovery_20260720.log", "24.GFOD2/scripts/server/03_gse288958_milestone01_audit.R", "24.GFOD2/scripts/server/04_gse288958_m01b_sensitivity.R", "24.GFOD2/scripts/server/05_export_gse288958_object_cells.R", "24.GFOD2/scripts/server/05_gse288958_scrublet_audit.py", "24.GFOD2/scripts/server/06_gse288958_scrublet_integration.R", "24.GFOD2/scripts/server/07_checksum_gse288958_raw_inputs.R", "24.GFOD2/scripts/server/21_planb_gse288958_analysis.R" ] } ], "result": { "dataset_bound_artifact_filename_hits": 4, "dataset_bound_exact_parameter_content_hits": 0, "proxy_or_audit_parameter_reference_hit_count": 4, "author_evidence_file_count": 0, "exact_author_command_found": false, "exact_sample_sheet_found": false, "exact_read_cycle_contract_found": false, "exact_barcode_whitelist_found": false, "exact_reference_package_found": false, "exact_fastq_aggregation_manifest_found": false, "conclusion": "No dataset-bound exact author Cell Ranger command, sample sheet, read-cycle contract, barcode whitelist, reference package checksum or FASTQ aggregation manifest was found in the searched local scopes. Proxy plans, audit scripts and reports are retained as references but do not count as author evidence. This is an inventory-limited negative result, not proof that the materials do not exist elsewhere." }, "non_binding_rule": "Do not transfer read structure, whitelist, reference package or command parameters from another accession or another project into GSE288958.", "next_action": "Request the six author-confirmation items listed in the processing contract before claiming author-exact raw reprocessing; they are optional for the bounded read-only processed-reference context release." }, "author_parameter_request": { "path": "neuromuscular_virtual_cell/data/external/GSE288958/author_parameter_request/gse288958_author_parameter_request.json", "response_template": "neuromuscular_virtual_cell/data/external/GSE288958/author_parameter_request/gse288958_author_parameter_response.template.json", "status": "AUTHOR_PARAMETER_REQUEST_PACKAGE_READY_RESPONSE_PENDING" }, "execution_authorization": { "source": "explicit user authorization in current task", "status_path": "data/external/GSE288958/metadata/gse288958_execution_status.json", "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false, "execution_state": { "sra_raw_reads": { "status": "DUPLICATE_DOWNLOAD_CLEANED_EXISTING_REFERENCE_RETAINED", "tool": "NCBI SRA Toolkit 3.0.5 prefetch plus vdb-validate", "run_count": 11, "target": "sra_runs/ (removed after duplicate-download cleanup)", "download_mode": "SRA Toolkit-native sparse/range-state resume on verified /personal archive symlink; maximum two concurrent runs after /share project-quota failures; 60-second heartbeat; vdb-validate and SHA-256 gates", "supervisor_pid": null, "retry_waiter_pid": null, "retry_waiter_script": "retry_gse288958_sra_after_first_pass.sh", "retry_waiter_sha256": "cdd6bd172e172d9e1b0979a6f4d6608c65d6956a379aee26ec6f62478d2ca5f9", "completed_runs": 0, "partial_runs": 0, "quarantined_mixed_resume_runs": [ "SRR32206095", "SRR32206096" ], "quarantine_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/quarantine_prefetch_mixed_resume_20260811/", "local_reads_present": false, "last_known_completed_runs": 7, "last_known_partial_runs": 4, "last_known_heartbeat": "2026-08-12T18:29:51+08:00", "blocker": null, "recovery_action": "User stopped and authorized cleanup of the duplicate SRA download route. The project-local native SRA directory, its symlink, stale locks and the quarantined duplicate partials were removed; the existing processed reference and all analysis artifacts were retained.", "toolkit_version": "3.0.5", "toolkit_root": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64", "prefetch_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/prefetch", "vdb_validate_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/vdb-validate", "fasterq_dump_path": "/personal/virtual_cell_dmd_20260706_archives/GSE288958_20260812/sratoolkit.3.0.5-ubuntu64/bin/fasterq-dump", "observed_resume_growth": "At 16:25, both active partial objects continued advancing. The 16:05:21–16:25:43 interval added approximately 30.4 MB combined (~24.9 KB/s); manifest-derived remaining partial volume is approximately 24.8 GB, giving a direct-rate estimate of about 11.5 days." }, "reference": { "status": "COMPLETE_CELLRANGER_PROXY_REFERENCE", "mode": "GRCh38 Ensembl release 113 proxy reference", "fasta": "Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz", "gtf": "Homo_sapiens.GRCh38.113.gtf.gz", "cellranger_reference_target": "cellranger_ref_GRCh38_Ensembl113_proxy_cr9", "build_policy": "gzip validation, atomic uncompressed materialization only when the Cell Ranger reference is incomplete; native genes/genes.gtf.gz is authoritative and uncompressed source material is archived after promotion", "build_result": "Cell Ranger 9 mkref completed successfully; the complete build directory was atomically promoted after all five gates passed", "author_reference_confirmed": false }, "raw_reprocessing": { "status": "NOT_REQUIRED_DUPLICATE_ROUTE_CLEANED_EXISTING_PROCESSED_REFERENCE_SUFFICIENT", "runner_pid": 53137, "runner_state": "REFERENCE_GATE_PASS; EXISTING_PROCESSED_REFERENCE_AVAILABLE; SRA_ROUTE_OPTIONAL", "planned_tool": "Cell Ranger 9.0.0 count", "planned_mode": "exploratory proxy reprocessing after SRA-to-FASTQ conversion", "sample_identity_contract": "normalized sample label plus explicit SRR/GSM mapping", "observed_sra_read_mapping": "read1=8bp technical index; read2=50bp biological Cell Ranger R1; read3=100bp biological Cell Ranger R2", "barcode_read_evidence": "SRR32206102 10,000-spot preflight: read2 first 16 bp exact 3M-february-2018_TRU whitelist match 9295/10000; read3 6/10000", "cellranger_chemistry_definition_check": "SC3Pv3-polyA uses R1[0:16] barcode, R1[16:28] UMI and R2 RNA from offset 0; 50bp R1 requires no pre-trimming", "fasterq_output_contract": "--skip-technical preserves original numbering; require _2.fastq.gz as R1 and _3.fastq.gz as R2", "per_run_fastq_gate": "10,000-record scan: fixed 50/100 bp lengths, exact paired IDs, >=0.50 R1 exact whitelist match and <=0.01 R2 match", "safe_handoff": "SRA-to-FASTQ proxy handoff is retained only for optional author-level reprocessing; it does not block existing-reference QC or context analysis", "required_output_gate": "FASTQ structure/whitelist audit, metrics, web summary, raw matrix/barcodes/features and filtered matrix/barcodes/features", "author_pipeline_reproduced": false }, "fastq_layout_preflight": { "status": "PASS_PROXY_READ_MAPPING_RECOVERED", "run": "SRR32206102", "spots_scanned": 10000, "sra_layout": "8bp technical + 50bp biological + 100bp biological", "fasterq_layout": "_2.fastq=50bp R1; _3.fastq=100bp R2", "paired_ids_match": true, "duplicate_ids": 0, "r1_exact_10x_v3_whitelist_fraction": 0.9295, "r2_exact_10x_v3_whitelist_fraction": 0.0006, "evidence_directory": "metadata/fastq_layout_preflight/SRR32206102/", "author_exact_read_contract_recovered": false }, "cellranger_subset_preflight": { "status": "PASS_STRUCTURAL_PROXY_COUNT", "run": "SRR32206102", "spots_scanned": 10000, "completed_at": "2026-08-11T23:14:57+08:00", "cellranger_version": "9.0.0", "reference": "cellranger_ref_GRCh38_Ensembl113_proxy_cr9", "r1_source": "_2.fastq.gz", "r2_source": "_3.fastq.gz", "metrics_summary": "preflight/cellranger_count_SRR32206102_10000_v2/SRR32206102_10000_cr9_preflight_v2/outs/metrics_summary.csv", "web_summary": "preflight/cellranger_count_SRR32206102_10000_v2/SRR32206102_10000_cr9_preflight_v2/outs/web_summary.html", "required_matrix_outputs": "PASS_raw_and_filtered_MEX_plus_HDF5", "structural_metrics": { "number_of_reads": 10000, "valid_barcodes": "93.8%", "valid_umis": "100.0%", "q30_barcode": "96.6%", "q30_rna": "94.9%", "q30_umi": "95.7%", "estimated_cells": 4991 }, "interpretation": "structural_only; no disease_effect_inference" }, "recovery_event": { "historical_failure_at": "2026-08-11T17:15:51+08:00", "historical_failure_stage": "reference_preparation_gate", "root_cause": "Cell Ranger 9 emitted genes/genes.gtf.gz while the preflight gate required genes/genes.gtf", "reference_build_itself": "SUCCESS", "recovery_at": "2026-08-11T22:51:58+08:00", "recovery_action": "promoted existing complete build without rebuilding STAR; removed the temporary invalid gzip-as-text alias after v1 count evidence and restarted the corrected native-gz proxy", "current_state": "RECOVERED_REFERENCE_COMPLETE_PROXY_WAITING_FOR_SRA" }, "formal_qc": { "status": "READY_EXISTING_REFERENCE_ROUTE", "runner_pid": 32314, "manifest_finalizer_pid": 32315, "runner_state": "WAITING_FOR_EXISTING_REFERENCE_QC_ROUTE; SRA_REPROCESSING_OPTIONAL", "planned_scope": "formal QC of the proxy reprocessing outputs", "input_preflight": "PASS_61189_PUBLISHED_MATRIX_CELLS_59222_PUBLISHED_OBJECT_CELLS_11_GSM", "required_packages_load_test": "PASS_DropletUtils_SingleCellExperiment_SummarizedExperiment_Matrix_scDblFinder_SoupX_scran_jsonlite", "started": false, "existing_reference_input": "formal_qc_input/existing_reference_raw_feature_bc_matrix/; 33 read-only links to the verified server-side 11-sample MEX reference", "author_formal_qc_reproduced": false }, "qc_dependencies": { "status": "COMPLETE", "bioconductor_target_version": "3.18 for R 4.3.3", "library": "formal_qc/r_lib_v2", "setup_pid_historical": 25407, "setup_process_state": "EXITED_AFTER_COMPLETE", "soupx": "PASS_1.6.2", "dropletutils": "PASS_1.22.0", "scdblfinder": "PASS_1.16.0", "completion_flag": "formal_qc/dependencies_v2.complete" }, "existing_processed_reference": { "status": "FOUND_AND_READ_ONLY_LINKED", "source_path": "LOCAL_WORKSPACE_PATH_WITHHELD/gse288958_human_muscle_reference", "link_path": "processed_reference_existing", "sample_count": 11, "matrix_count": 11, "barcode_count": 11, "feature_count": 11, "raw_archive_bytes": 359823360, "annotated_rds_bytes": 1847703081, "annotated_rds_sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "raw_archive_sha256_remote": "782f3a18097caec58efd741253a1186598906e67c777dd3ec98066096bb86f91", "raw_archive_sha256_local_record": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "raw_archive_byte_identity": "NOT_ESTABLISHED_SAME_SIZE_MEMBER_AND_GZIP_VALIDATION_ONLY", "gzip_validation": "PASS", "tar_member_count": 32, "role": "existing_processed_reference_reuse; does_not_replace_author_exact_SRA_reprocessing" }, "existing_reference_preflight": { "status": "PASS_11_OF_11_SAMPLES", "report": "metadata/existing_reference_preflight/gse288958_existing_reference_preflight.json", "sample_report": "metadata/existing_reference_preflight/gse288958_existing_reference_sample_qc.tsv", "checked_at": "2026-08-12T14:20:00+08:00", "checks": [ "matrix_rows_equal_feature_rows", "matrix_cols_equal_barcode_rows", "barcode_unique", "feature_count_36601", "shared_feature_content_sha256" ], "all_sample_structural_checks_pass": true, "total_matrix_cells": 61189, "next_route": "existing_reference_qc_and_annotation_audit", "claim_boundary": "Structural reuse preflight only; not author-exact Cell Ranger reproduction, not formal ambient/doublet QC, and not direct DMD perturbation truth." }, "existing_reference_qc_risk_audit": { "status": "PASS_WITH_NORMAL_2_LOW_COMPLEXITY_FLAG", "report": "metadata/existing_reference_preflight/qc_risk_audit.md", "source_filter_summary": "metadata/existing_reference_preflight/gse288958_filter_summary_by_sample.tsv", "flagged_sample": "Normal_2", "flagged_sample_raw_cells": 4953, "flagged_sample_retained_cells": 3020, "flagged_sample_retained_percent": 62.0123203285421, "flagged_sample_median_nCount_RNA": 589, "flagged_sample_median_nFeature_RNA": 406, "other_sample_retained_percent_range": "99.662984459839-100", "next_route": "sample_aware_context_qc_with_predeclared_Normal_2_sensitivity", "claim_boundary": "QC risk flag only; no ad hoc sample deletion, no disease-effect inference, and formal ambient/doublet/final annotation gates remain unresolved." }, "existing_matrix_qc_audit": { "status": "COMPLETE_READ_ONLY_MATRIX_AUDIT", "report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_audit.md", "sample_report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_sample.tsv", "cell_report": "metadata/existing_reference_preflight/existing_matrix_qc_audit/existing_matrix_qc_by_cell.tsv.gz", "checked_at": "2026-08-12T17:10:00+08:00", "sample_count": 11, "total_raw_cells": 61189, "total_broad_gate_retained_cells": 59252, "broad_gate": "nFeature_RNA >= 300 and <= 8000; nCount_RNA >= 500; percent.mt <= 10", "flagged_sample": "Normal_2", "flagged_sample_retained_percent": 61.15485564304461, "claim_boundary": "Independent matrix-level QC audit of the existing processed reference; not author-exact Cell Ranger reproduction, not complete ambient/doublet calling, and not direct DMD perturbation truth." }, "existing_reference_formal_qc_audit": { "status": "COMPLETE_MATRIX_QC_LOW_COUNT_AMBIENT_PROFILE_MARKER_AUDIT_SOUPX_DOUBLETS_PENDING", "report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_report.json", "sample_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_by_sample.tsv", "ambient_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_ambient_estimates.tsv", "cell_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_formal_cell_qc.tsv.gz", "annotation_report": "formal_qc_input/existing_reference_qc_audit/existing_reference_independent_annotation_counts.tsv", "checked_at": "2026-08-12T17:50:10+08:00", "sample_count": 11, "total_raw_cells": 61189, "total_broad_gate_retained_cells": 59237, "emptydrops_status": "UNAVAILABLE_NO_UNFILTERED_EMPTY_DROPLET_COUNTS;LOW_COUNT_AMBIENT_PROFILE_RETAINED_AS_PROXY", "soupx_status": "PENDING_TASK_LOCAL_PACKAGE_RUNTIME", "scdblfinder_status": "PENDING_TASK_LOCAL_PACKAGE_RUNTIME", "flagged_sample": "Normal_2", "claim_boundary": "Read-only existing-reference audit only. Broad gate, low-count ambient profile and independent marker scores are descriptive. This is not author-exact Cell Ranger reproduction, not complete ambient/doublet closure and not disease-effect truth." }, "existing_reference_context_sensitivity": { "status": "PASS_DESCRIPTIVE_SAMPLE_AWARE_WITH_NORMAL_2_SENSITIVITY", "report_json": "metadata/existing_reference_preflight/gse288958_sample_aware_context_sensitivity/gse288958_sample_aware_context_sensitivity.json", "report_tsv": "metadata/existing_reference_preflight/gse288958_sample_aware_context_sensitivity/gse288958_sample_aware_context_sensitivity.tsv", "checked_at": "2026-08-12T14:35:00+08:00", "statistical_unit": "sample_level_module_mean", "direction_preserved_modules": [ "FAP_fibroblast:FAP_ECM_fibrosis", "FAP_fibroblast:regeneration_stress", "macrophage_monocyte:macrophage_inflammatory_state", "myonuclei_contractile:oxidative_mito_score", "myonuclei_contractile:regeneration_stress", "satellite_myogenic:regeneration_stress" ], "direction_flip_modules": [ "macrophage_monocyte:TLR2_NOD2_sensing" ], "interpretation": "FAP/ECM fibrosis, myonuclear regeneration/stress and macrophage inflammatory context are directionally retained; macrophage TLR2/NOD2 is unstable to Normal_2 exclusion and must not be claimed as robust DMD-dominant context.", "claim_boundary": "Descriptive context sensitivity only; no p-values, disease-effect authorization, causality or direct DMD perturbation truth." } } }, "confirmed_fields": { "assay_context": "single-nucleus RNA-seq from flow-cytometry-isolated nuclei", "library_chemistry": { "platform": "10x Genomics Single Cell Chromium 3'", "version": "V3", "protocol_id": "CG000183" }, "sequencing": { "layout": "PAIRED", "reported_read_specification": "paired-end 200 bp reads", "platform": "ILLUMINA", "instrument_model": "Illumina NovaSeq 6000", "exact_read_cycle_allocation": null }, "published_processing": { "software": "Cell Ranger", "version": "6.0.0", "reference_as_reported": "human GRCh38/hg38 pre-mRNA genome transcriptome references provided by 10x Genomics", "assembly": "GRCh38/hg38", "output_format_as_reported": [ "tsv", "mtx" ] } }, "author_confirmation_required": { "exact_read_cycle_allocation": "Need R1/i7/i5/R2 cycle counts or the original Cell Ranger sample sheet; the SOFT reports paired-end 200 bp but does not expose cycle allocation.", "barcode_whitelist": "Need the exact 10x whitelist/version used by the original Cell Ranger run, including whether chemistry-specific auto-detection was used.", "reference_package": "Need the exact 10x reference package identifier, release date/version and checksum; the SOFT identifies GRCh38/hg38 pre-mRNA but not a package checksum.", "feature_reference": "Need confirmation whether any feature-reference CSV was used; the public supplement is a gene feature table, not proof of a Cell Ranger feature-reference input.", "command_and_parameters": "Need the original Cell Ranger command/sample sheet and any intronic, chemistry, cell-calling or aggregation parameters.", "fastq_manifest": "Need confirmation of FASTQ naming, lane/run aggregation and per-sample library IDs before reprocessing." }, "gates": { "source_method_evidence_present": true, "chemistry_identified": true, "reference_family_identified": true, "published_cellranger_version_identified": true, "exact_read_cycle_allocation_confirmed": false, "barcode_whitelist_confirmed": false, "reference_package_checksum_confirmed": false, "original_command_confirmed": false, "processing_contract_complete": false, "raw_reprocessing_authorized": false, "formal_qc_authorized": false, "disease_effect_test_authorized": false }, "next_action": "Use the published Cell Ranger 6.0.0 and GRCh38/hg38 pre-mRNA statements as official processing context. Bind the six exact author artifacts only before claiming author-exact reprocessing; they are optional for bounded read-only reference use.", "claim_boundary": "The contract records the official published processing recipe and separates it from unresolved author-exact execution artifacts. The existing-reference audit may support bounded read-only context, while author-exact reproduction, author QC and DMD candidate perturbation truth remain unclaimed." } }, { "artifact_id": "raw_cell_inventory", "state": "PRESENT", "candidate_names": [ "raw_cell_inventory.csv", "gse288958_raw_cell_inventory.csv", "cell_inventory.csv" ], "path": "raw_cell_inventory.csv", "size_bytes": 12899748, "sha256": "98e63692a9bf08dbdcb6d5ef521108dfe4f99500da55ee4b5752cae7e735143f", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "headers": [ "sample_id", "barcode", "cell_id", "donor_id", "disease", "biopsy_site", "age", "batch", "donor_id_status", "cell_type", "annotation_source", "annotation_status", "sample_cell_index" ] }, { "artifact_id": "feature_table", "state": "MISSING", "candidate_names": [ "features.tsv.gz", "features.tsv", "genes.tsv.gz", "genes.tsv" ], "path": null, "size_bytes": null, "sha256": null, "missing_fields": [], "notes": "Required portable-import object is not present in the candidate directory." }, { "artifact_id": "barcode_table", "state": "MISSING", "candidate_names": [ "barcodes.tsv.gz", "barcodes.tsv", "cell_barcodes.tsv" ], "path": null, "size_bytes": null, "sha256": null, "missing_fields": [], "notes": "Required portable-import object is not present in the candidate directory." }, { "artifact_id": "provenance_manifest", "state": "PRESENT", "candidate_names": [ "provenance.json", "import_manifest.json" ], "path": "import_manifest.json", "size_bytes": 4313, "sha256": "bc72c7e660c004738116b7f9542b984a9b08d0bfc13e3f60c2d7ac4b2dfa8687", "missing_fields": [], "notes": "File is present and checksum-addressed; opening and cross-object reconciliation remain separate gates.", "json": { "manifest_schema": "nmd-vcell-gse288958-multisample-source-package/1.0", "dataset_id": "GSE288958", "accession": "GSE288958", "package_type": "MULTI_SAMPLE_10X_MTX_TSV_SOURCE_PACKAGE", "source_archive": { "path": "../raw/GSE288958_RAW.tar", "size_bytes": 359823360, "sha256": "fdbe0cefc3f169e112808746d8fd418927893828d40880ea325aecd3561b1931", "tar_member_count": 32, "gzip_streams_passed": 32 }, "feature_supplement": { "path": "../raw/GSE288958_BMD_1_features.tsv.gz", "size_bytes": 333437, "sha256": "f99a146106e8e37a1bf5933e9ee3bc84139ffee889540ea0425fd3f9fbeef4a7", "gzip_validation": "PASS" }, "sample_metadata": { "path": "sample_metadata.csv", "source": "../metadata/GSE288958_family_soft_sample_metadata.csv", "rows": 11, "donor_id_state": "SAMPLE_ACCESSION_PROXY_NOT_SUBJECT_IDENTIFIER", "batch_state": "NOT_REPORTED_IN_FAMILY_SOFT" }, "sample_units": [ { "sample_id": "GSM8779827", "disease": "control", "matrix_member": "GSM8779827_Normal_1_matrix.mtx.gz", "barcode_member": "GSM8779827_Normal_1_barcodes.tsv.gz", "feature_member": "GSM8779827_Normal_1_features.tsv.gz" }, { "sample_id": "GSM8779828", "disease": "control", "matrix_member": "GSM8779828_Normal_2_matrix.mtx.gz", "barcode_member": "GSM8779828_Normal_2_barcodes.tsv.gz", "feature_member": "GSM8779828_Normal_2_features.tsv.gz" }, { "sample_id": "GSM8779829", "disease": "control", "matrix_member": "GSM8779829_Normal_3_matrix.mtx.gz", "barcode_member": "GSM8779829_Normal_3_barcodes.tsv.gz", "feature_member": "GSM8779829_Normal_3_features.tsv.gz" }, { "sample_id": "GSM8779830", "disease": "control", "matrix_member": "GSM8779830_Normal_4_matrix.mtx.gz", "barcode_member": "GSM8779830_Normal_4_barcodes.tsv.gz", "feature_member": "GSM8779830_Normal_4_features.tsv.gz" }, { "sample_id": "GSM8779831", "disease": "control", "matrix_member": "GSM8779831_Normal_5_matrix.mtx.gz", "barcode_member": "GSM8779831_Normal_5_barcodes.tsv.gz", "feature_member": "GSM8779831_Normal_5_features.tsv.gz" }, { "sample_id": "GSM8779832", "disease": "BMD", "matrix_member": "GSM8779832_BMD_1_matrix.mtx.gz", "barcode_member": "GSM8779832_BMD_1_barcodes.tsv.gz", "feature_member": "../raw/GSE288958_BMD_1_features.tsv.gz" }, { "sample_id": "GSM8779833", "disease": "BMD", "matrix_member": "GSM8779833_BMD_2_matrix.mtx.gz", "barcode_member": "GSM8779833_BMD_2_barcodes.tsv.gz", "feature_member": "GSM8779833_BMD_2_features.tsv.gz" }, { "sample_id": "GSM8779834", "disease": "BMD", "matrix_member": "GSM8779834_BMD_3_matrix.mtx.gz", "barcode_member": "GSM8779834_BMD_3_barcodes.tsv.gz", "feature_member": "GSM8779834_BMD_3_features.tsv.gz" }, { "sample_id": "GSM8779835", "disease": "DMD", "matrix_member": "GSM8779835_DMD_1_matrix.mtx.gz", "barcode_member": "GSM8779835_DMD_1_barcodes.tsv.gz", "feature_member": "GSM8779835_DMD_1_features.tsv.gz" }, { "sample_id": "GSM8779836", "disease": "DMD", "matrix_member": "GSM8779836_DMD_2_matrix.mtx.gz", "barcode_member": "GSM8779836_DMD_2_barcodes.tsv.gz", "feature_member": "GSM8779836_DMD_2_features.tsv.gz" }, { "sample_id": "GSM8779837", "disease": "DMD", "matrix_member": "GSM8779837_DMD_3_matrix.mtx.gz", "barcode_member": "GSM8779837_DMD_3_barcodes.tsv.gz", "feature_member": "GSM8779837_DMD_3_features.tsv.gz" } ], "annotation_state": "CANDIDATE_COARSE_CELLTYPE_EXPORT_PARTIAL_SENSITIVITY_AUDIT_NOT_FINAL", "annotation_object": { "path": "cell_annotations.csv", "provenance_path": "candidate_annotation_provenance.json", "object_path": "../objects/gse288958_reference_qc_umap_annotated.rds", "object_open_audit_path": "object_open_audit.json", "partial_annotation_audit_path": "annotation_audit.json", "rows": 59222, "source_object_sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "source_object_local_state": "LOCAL_RDS_PRESENT_SHA256_VERIFIED_AND_OPENED", "annotation_level": "coarse_celltype", "annotation_audit_state": "PARTIAL_ANNOTATION_SENSITIVITY_AUDIT_FORMAL_DOUBLET_AMBIENT_UNRESOLVED" }, "provenance_state": "SOURCE_ARCHIVE_AND_GEO_SOFT_CHECKSUMMED", "object_open_state": "LOCAL_RDS_OPENED_CELL_SAMPLE_METADATA_AND_FEATURE_IDENTIFIERS_RECONCILED", "analysis_authorization": "BLOCKED_UNTIL_FORMAL_DOUBLET_AMBIENT_FINAL_ANNOTATION_AND_PROVENANCE_REVIEW", "direct_dmd_candidate_perturbation_truth": "0/21" } } ], "gates": { "source_object_present": true, "source_package_manifest_present": true, "workspace_local_path": true, "sample_metadata_schema": true, "raw_cell_inventory_present": true, "raw_cell_inventory_schema": true, "cell_annotation_schema": true, "annotation_provenance_present": true, "candidate_annotation_ids_reconciled": true, "feature_barcode_objects": true, "provenance_manifest_present": true, "source_object_opened": true, "identifiers_reconciled": true, "partial_annotation_audit": true, "formal_qc_input_request_present": true, "formal_qc_input_manifest_present": false, "formal_qc_input_preflight_present": true, "sra_recovery_manifest_present": true, "parameter_recovery_audit_present": true, "author_parameter_request_present": true, "processing_contract_present": true, "annotation_audited": true, "independent_doublet_audit": true, "independent_annotation_audit": true, "formal_ambient_audit": false, "disease_effect_test_authorized": false, "direct_dmd_candidate_perturbation_truth": false }, "pilot_reference": { "cells": 59222, "samples": 11, "selected_compartment": "endothelial", "selection_uses_disease_labels": false, "verdict": "PASS_FOR_VALIDATION_PILOT", "scope": "Validation pilot only; not the independent primary discovery cohort." }, "next_action": "Run the bounded read-only sample-aware context route with Normal_2, Scrublet and annotation-disagreement sensitivities. Ambient RNA and author-exact reprocessing remain separate optional enhancement gates.", "claim_boundary": "Object opening, identifier reconciliation, donor-wise doublet sensitivity and independent marker-label disagreement audits support bounded read-only sample-aware context. Ambient RNA remains unresolved, author-exact reprocessing remains unclaimed, and disease-effect, causality, therapeutic and direct DMD perturbation claims stay locked.", "direct_dmd_candidate_perturbation_truth": "0/21" }, "gse288958_qc_gate": { "registry_schema": "nmd-vcell-gse288958-qc-gate/2.0", "dataset_id": "GSE288958", "accession": "GSE288958", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-12T18:15:46+0800", "status": "REFERENCE_CONTEXT_READY_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN", "context_release_ready": true, "context_release_blocking_open_gate_count": 0, "enhancement_open_gate_count": 2, "source_object": { "path": "neuromuscular_virtual_cell/data/external/GSE288958/objects/gse288958_reference_qc_umap_annotated.rds", "sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "class": "Seurat", "cells": 59222, "features": 29242, "opened": true, "identifiers_reconciled": true }, "design": { "samples": 11, "conditions": { "control": 5, "bmd": 3, "dmd": 3 }, "inferential_unit": "independent biopsy/sample; cells remain nested observations", "denominator": { "raw_matrix_cells": 61189, "formal_qc_broad_gate_retained_cells": 59237, "qc_context_gate_retained_cells": 59237, "pilot_rds_cells": 59222, "raw_minus_pilot_cells": 1967, "formal_qc_minus_pilot_cells": 15, "reconciliation_note": "The 61,189 raw-cell inventory, formal matrix-QC denominator and 59,222-cell pilot RDS are preserved as separate denominators; no silent promotion or deletion is performed." } }, "reference_audit": { "audit_id": "GSE288958:REFERENCE-AUDIT:20260909:1", "supersedes_partial_audit_level": "PARTIAL_ANNOTATION_AND_SENSITIVITY_AUDIT", "api_route": "/resource/api/v1.1/gse288958_reference_audit.json", "web_route": "/resource/gse288958-audit/", "independent_doublet_candidates": 1579, "independent_doublet_fraction": 0.026662388977069334, "independent_annotation_resolved_cells": 58912, "independent_annotation_unresolved_cells": 310, "independent_annotation_concordance_fraction_resolved": 0.7588606735469854 }, "matrix_qc": { "status": "COMPLETE_MATRIX_QC_LOW_COUNT_AMBIENT_PROFILE_MARKER_AUDIT", "gate": "nFeature_RNA >= 300 and <= 8000; nCount_RNA >= 500; percent.mt <= 10", "flagged_sample": "Normal_2", "flagged_sample_retained_percent": 61.1548556430446, "sample_summary": { "Normal_1": { "disease": "control", "raw_cells": 9170, "retained_cells": 9166, "retained_percent": 99.9563794983642, "median_nCount_RNA": 4140, "median_nFeature_RNA": 1851, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_2": { "disease": "control", "raw_cells": 4953, "retained_cells": 3029, "retained_percent": 61.1548556430446, "median_nCount_RNA": 582, "median_nFeature_RNA": 403, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_3": { "disease": "control", "raw_cells": 6644, "retained_cells": 6644, "retained_percent": 100, "median_nCount_RNA": 2528, "median_nFeature_RNA": 1145, "median_percent_mt": 0.0391696103966241, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_4": { "disease": "control", "raw_cells": 3775, "retained_cells": 3774, "retained_percent": 99.9735099337748, "median_nCount_RNA": 5197, "median_nFeature_RNA": 2164, "median_percent_mt": 0.0791318109880172, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "Normal_5": { "disease": "control", "raw_cells": 4623, "retained_cells": 4621, "retained_percent": 99.956738048886, "median_nCount_RNA": 4463, "median_nFeature_RNA": 1912, "median_percent_mt": 0.0874635568513119, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_1": { "disease": "BMD", "raw_cells": 5521, "retained_cells": 5521, "retained_percent": 100, "median_nCount_RNA": 1332, "median_nFeature_RNA": 859, "median_percent_mt": 0, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_2": { "disease": "BMD", "raw_cells": 8615, "retained_cells": 8613, "retained_percent": 99.9767846778874, "median_nCount_RNA": 2814, "median_nFeature_RNA": 1311, "median_percent_mt": 0.111141983884412, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "BMD_3": { "disease": "BMD", "raw_cells": 5341, "retained_cells": 5323, "retained_percent": 99.662984459839, "median_nCount_RNA": 3233, "median_nFeature_RNA": 1629, "median_percent_mt": 0.955667640031856, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_1": { "disease": "DMD", "raw_cells": 3368, "retained_cells": 3368, "retained_percent": 100, "median_nCount_RNA": 1874.5, "median_nFeature_RNA": 1225, "median_percent_mt": 0.0354547612080036, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_2": { "disease": "DMD", "raw_cells": 3063, "retained_cells": 3062, "retained_percent": 99.9673522690173, "median_nCount_RNA": 4742, "median_nFeature_RNA": 2235, "median_percent_mt": 0.146627565982405, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" }, "DMD_3": { "disease": "DMD", "raw_cells": 6116, "retained_cells": 6116, "retained_percent": 100, "median_nCount_RNA": 2965.5, "median_nFeature_RNA": 1625, "median_percent_mt": 0.284023684550187, "low_count_ambient_profile": "low_count_proxy_when_unfiltered_droplets_unavailable" } } }, "context_gate": { "stable_modules": [ "FAP_fibroblast:FAP_ECM_fibrosis", "FAP_fibroblast:regeneration_stress", "macrophage_monocyte:macrophage_inflammatory_state", "myonuclei_contractile:oxidative_mito_score", "myonuclei_contractile:regeneration_stress", "satellite_myogenic:regeneration_stress" ], "unstable_modules": [ "macrophage_monocyte:TLR2_NOD2_sensing" ], "candidate_context_only": [ "ADAM10", "CPEB1" ], "normal_2_sensitivity_required": true, "disease_effect_testing_authorized": false, "model_training_labels_allowed": false, "direct_dmd_perturbation_truth": false }, "gates": [ { "gate": "source_object_and_identifiers", "state": "PASS", "evidence": "Seurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled", "closure_required": "None for pilot context; keep the SHA-addressed source object immutable" }, { "gate": "official_processing_metadata", "state": "PASS_PARTIAL_OFFICIAL", "evidence": "GEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples", "closure_required": "Keep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable" }, { "gate": "matrix_qc", "state": "PASS_READ_ONLY", "evidence": "11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity", "closure_required": "Author-exact Cell Ranger/QC reproduction is optional and must remain separate from this route" }, { "gate": "ambient_rna", "state": "OPEN_FORMAL_AMBIENT", "evidence": "Low-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable", "closure_required": "Unfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit" }, { "gate": "doublet", "state": "PASS_INDEPENDENT_SENSITIVITY", "evidence": "Donor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL", "closure_required": "Retain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels" }, { "gate": "independent_annotation", "state": "PASS_INDEPENDENT_AUDIT_BOUNDED", "evidence": "Fixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89%", "closure_required": "Keep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap" }, { "gate": "author_exact_reprocessing", "state": "OPEN_OPTIONAL_AUTHOR_CONFIRMATION", "evidence": "Public software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit", "closure_required": "Required only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse" }, { "gate": "sample_aware_context", "state": "PASS_DESCRIPTIVE_ONLY", "evidence": "6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only", "closure_required": "Use all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels" } ], "operational_boundary": { "sra_route": "DUPLICATE_DOWNLOAD_CLEANED_EXISTING_REFERENCE_RETAINED", "sra_download_required": false, "author_exact_reprocessing": false, "formal_qc_input_preflight": "FORMAL_QC_INPUTS_MANIFEST_MISSING_RETAINED_FOR_AMBIENT_AND_AUTHOR_EXACT_PROMOTION_ONLY", "direct_dmd_candidate_perturbation_truth": "0/21" }, "source_artifacts": { "object_open_audit": { "role": "object_open_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/object_open_audit.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 4234, "sha256": "282a11d6cf69f5e17326b1b7516f785ff8a8327a6b46cac11b49fab2cdfd7833" }, "annotation_audit": { "role": "annotation_audit", "path": "neuromuscular_virtual_cell/data/external/GSE288958/import/annotation_audit.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 5708, "sha256": "5df910ea15f644d4a3e104983def2be528f1b1bbade46e0e8b73236c5ec08596" }, "formal_qc_report": { "role": "formal_qc_report", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_report.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 1423, "sha256": "94c0385cf5898ad330d9f41340de5e1f565b00e0189f9e8cab6bf4fc4a4f8d3b" }, "sample_qc": { "role": "sample_qc", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_formal_qc_by_sample.tsv", "state": "FORMAL_QC_AUDIT_TABLE_CHECKSUMMED", "size_bytes": 3046, "sha256": "4493cfc7f8b2bab95d2f46ab80ff672e66cbe78cb3635d8fe36c5b3f442233ca" }, "ambient_estimates": { "role": "ambient_estimates", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/existing_reference_qc_audit/existing_reference_ambient_estimates.tsv", "state": "FORMAL_QC_AUDIT_TABLE_CHECKSUMMED", "size_bytes": 3783, "sha256": "4c722021acad830538a1ed8381564a98c1e5098feaa167a3c4b397654eb4a4fd" }, "qc_context_gate": { "role": "qc_context_gate", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/qc_context_gate/gse288958_qc_context_gate.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 10513, "sha256": "f28edc8e9baa9b0f8914f849b98869964931911d677adfad0bf1bfaef35761e8" }, "formal_qc_preflight": { "role": "formal_qc_preflight", "path": "neuromuscular_virtual_cell/data/external/GSE288958/formal_qc_input/formal_qc_input_preflight.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 2080, "sha256": "1b2a08084c9030d76480e282e1992cff773dd00d8c3f121ddf52ca1acbccb785" }, "execution_status": { "role": "execution_status", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/gse288958_execution_status.json", "state": "FORMAL_QC_GATE_INPUT_CHECKSUMMED", "size_bytes": 24920, "sha256": "87a88c6098dff3951471190a23865ed9e43037249b593ecf5c02c2295838e9ef" } }, "claim_boundary": "GSE288958 supports bounded read-only, sample-aware descriptive context with predeclared Normal_2, donor-wise Scrublet and annotation-disagreement sensitivities. Ambient RNA remains unresolved, author-exact Cell Ranger reproduction remains unclaimed, and disease-effect testing, causal claims, model-training labels, therapeutic efficacy and direct DMD perturbation truth remain locked.", "next_action": "Use the reference context with visible Normal_2, Scrublet and annotation-disagreement sensitivities. Seek unfiltered droplets only for ambient-RNA closure and the six exact author artifacts only before an author-exact reprocessing claim.", "markdown": "# GSE288958 formal QC gate\n\n- Status: **REFERENCE_CONTEXT_READY_INDEPENDENT_AUDITS_COMPLETE_AMBIENT_OPEN**\n- Checked: 2026-08-12T18:15:46+0800\n- Source object: `ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8`\n- Context-release blocking open gates: **0**\n\n## Current decision\n\nUse the reference context with visible Normal_2, Scrublet and annotation-disagreement sensitivities. Seek unfiltered droplets only for ambient-RNA closure and the six exact author artifacts only before an author-exact reprocessing claim.\n\n## Denominator reconciliation\n\n- Raw matrix inventory: **61,189** cells\n- Formal matrix-QC broad gate: **59,237** cells\n- Pilot RDS: **59,222** cells\n- Raw minus pilot: **1,967** cells\n\nThe 61,189 raw-cell inventory, formal matrix-QC denominator and 59,222-cell pilot RDS are preserved as separate denominators; no silent promotion or deletion is performed.\n\n## Gate table\n\n| Gate | State | Evidence | Closure required |\n|---|---|---|---|\n| source_object_and_identifiers | PASS | Seurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled | None for pilot context; keep the SHA-addressed source object immutable |\n| official_processing_metadata | PASS_PARTIAL_OFFICIAL | GEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples | Keep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable |\n| matrix_qc | PASS_READ_ONLY | 11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity | Author-exact Cell Ranger/QC reproduction is optional and must remain separate from this route |\n| ambient_rna | OPEN_FORMAL_AMBIENT | Low-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable | Unfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit |\n| doublet | PASS_INDEPENDENT_SENSITIVITY | Donor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL | Retain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels |\n| independent_annotation | PASS_INDEPENDENT_AUDIT_BOUNDED | Fixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89% | Keep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap |\n| author_exact_reprocessing | OPEN_OPTIONAL_AUTHOR_CONFIRMATION | Public software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit | Required only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse |\n| sample_aware_context | PASS_DESCRIPTIVE_ONLY | 6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only | Use all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels |\n\n## Independent audits\n\nDonor-wise Scrublet covers **59,222** cells and flags **1,579** candidates. Fixed-marker annotation resolves **58,912** cells, keeps **310** unresolved and reports **75.89%** resolved-label concordance with harmonized inherited labels.\n\n## Allowed use\n\nGSE288958 supports bounded read-only, sample-aware descriptive context with predeclared Normal_2, donor-wise Scrublet and annotation-disagreement sensitivities. Ambient RNA remains unresolved, author-exact Cell Ranger reproduction remains unclaimed, and disease-effect testing, causal claims, model-training labels, therapeutic efficacy and direct DMD perturbation truth remain locked.\n\nDirect DMD candidate perturbation truth remains **0/21**.\n", "tsv": "gate\tstate\tevidence\tclosure_required\nsource_object_and_identifiers\tPASS\tSeurat opened; 59,222 cells × 29,242 features; sample/cell/feature identifiers reconciled\tNone for pilot context; keep the SHA-addressed source object immutable\nofficial_processing_metadata\tPASS_PARTIAL_OFFICIAL\tGEO reports Cell Ranger 6.0.0 and human GRCh38/hg38 pre-mRNA genome for all 11 samples\tKeep the exact author command, read structure, whitelist, reference checksum, sample sheet and aggregation manifest explicitly unavailable\nmatrix_qc\tPASS_READ_ONLY\t11 samples; broad gate retains 59,237 cells; Normal_2 is predeclared low-complexity/high-filter-loss sensitivity\tAuthor-exact Cell Ranger/QC reproduction is optional and must remain separate from this route\nambient_rna\tOPEN_FORMAL_AMBIENT\tLow-count ambient profile exists as a proxy; emptyDrops and SoupX autoEstCont are not complete; unfiltered droplets are unavailable\tUnfiltered droplets/raw_feature_bc_matrix or author contamination estimates, then emptyDrops/SoupX audit\ndoublet\tPASS_INDEPENDENT_SENSITIVITY\tDonor-wise Scanpy Scrublet covers 59,222 object cells and flags 1,579 candidates; isolated rerun is IDENTICAL\tRetain calls as an independent sensitivity layer and do not overwrite the baseline object or present algorithmic candidates as author labels\nindependent_annotation\tPASS_INDEPENDENT_AUDIT_BOUNDED\tFixed-marker scoring covers 59,222 object cells; 310 remain unresolved and resolved-label concordance is 75.89%\tKeep inherited and analyst labels distinct, preserve every disagreement and retain the B/plasma panel gap\nauthor_exact_reprocessing\tOPEN_OPTIONAL_AUTHOR_CONFIRMATION\tPublic software and reference family are known; the six exact author execution artifacts remain unavailable after provenance-aware audit\tRequired only before an author-exact Cell Ranger reproduction claim; not required for bounded read-only context reuse\nsample_aware_context\tPASS_DESCRIPTIVE_ONLY\t6 stable modules, 1 unstable module; ADAM10/CPEB1 remain module-level context only\tUse all-sample and Normal_2-excluded summaries; no disease-effect p-values or model labels\ndenominator\traw_matrix_cells\t61189\tPreserve raw-versus-pilot denominator gap\ndenominator\tformal_qc_broad_gate_retained_cells\t59237\tKeep formal QC and pilot RDS as distinct objects\ndenominator\tpilot_rds_cells\t59222\tDo not promote pilot denominator silently\n" }, "gse288958_context_object": { "registry_schema": "nmd-vcell-context-object/1.1", "object_id": "CONTEXT:GSE288958:SAMPLE_AWARE_MODULE:1.1", "object_type": "SAMPLE_AWARE_DESCRIPTIVE_CONTEXT", "lifecycle_status": "CITABLE_BOUNDED_REFERENCE_CONTEXT_INDEPENDENT_AUDITS_COMPLETE", "resource_release": "v1.2.0-measured-dmd-evidence", "evidence_freeze": "2026-08-03", "interface_build": "EA-20260817-57", "checked_at": "2026-08-12T18:15:46+0800", "dataset_id": "GSE288958", "accession": "GSE288958", "source_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288958", "evidence_state": "DESCRIPTIVE_SAMPLE_AWARE_REFERENCE_CONTEXT_WITH_NORMAL_2_DOUBLET_AND_ANNOTATION_SENSITIVITIES", "public_state": "SUMMARY_TABLES_ONLY_SOURCE_MATRIX_NOT_REHOSTED", "context_role": "DMD/BMD/control muscle sample-aware context reuse from the existing processed reference", "inferential_unit": "independent biopsy/sample; cells are nested observations and not independent disease replicates", "design": { "samples": 11, "conditions": { "control": 5, "bmd": 3, "dmd": 3 }, "raw_cells": 61189, "broad_gate_retained_cells": 59237, "pilot_rds_cells": 59222, "raw_minus_pilot_cells": 1967, "normal_2_policy": "Retain Normal_2 in all-sample descriptive summaries; repeat the context summary excluding Normal_2 as a predeclared sensitivity." }, "source_object": { "path": "neuromuscular_virtual_cell/data/external/GSE288958/objects/gse288958_reference_qc_umap_annotated.rds", "sha256": "ff4e34c69db855640d9091cc6c1981d85b8a51fefe7c1cf40a54336bad0b4fa8", "class": "Seurat", "cells": 59222, "features": 29242, "opened": true, "identifiers_reconciled": true }, "sample_units": [ { "sample_id": "Normal_1", "gsm": "GSM8779827", "condition": "control", "raw_cells": 9170, "broad_gate_retained_cells": 9166, "broad_gate_retained_percent": 99.9563794983642, "median_nCount_RNA": 4140, "median_nFeature_RNA": 1851, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "Normal_2", "gsm": "GSM8779828", "condition": "control", "raw_cells": 4953, "broad_gate_retained_cells": 3029, "broad_gate_retained_percent": 61.1548556430446, "median_nCount_RNA": 582, "median_nFeature_RNA": 403, "matrix_qc_status": "FLAG_LOW_COMPLEXITY", "normal_2_flag": true, "context_role": "SENSITIVITY_ONLY_FLAGGED_SAMPLE" }, { "sample_id": "Normal_3", "gsm": "GSM8779829", "condition": "control", "raw_cells": 6644, "broad_gate_retained_cells": 6644, "broad_gate_retained_percent": 100, "median_nCount_RNA": 2528, "median_nFeature_RNA": 1145, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "Normal_4", "gsm": "GSM8779830", "condition": "control", "raw_cells": 3775, "broad_gate_retained_cells": 3774, "broad_gate_retained_percent": 99.9735099337748, "median_nCount_RNA": 5197, "median_nFeature_RNA": 2164, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "Normal_5", "gsm": "GSM8779831", "condition": "control", "raw_cells": 4623, "broad_gate_retained_cells": 4621, "broad_gate_retained_percent": 99.956738048886, "median_nCount_RNA": 4463, "median_nFeature_RNA": 1912, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "BMD_1", "gsm": "GSM8779832", "condition": "BMD", "raw_cells": 5521, "broad_gate_retained_cells": 5521, "broad_gate_retained_percent": 100, "median_nCount_RNA": 1332, "median_nFeature_RNA": 859, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "BMD_2", "gsm": "GSM8779833", "condition": "BMD", "raw_cells": 8615, "broad_gate_retained_cells": 8613, "broad_gate_retained_percent": 99.9767846778874, "median_nCount_RNA": 2814, "median_nFeature_RNA": 1311, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "BMD_3", "gsm": "GSM8779834", "condition": "BMD", "raw_cells": 5341, "broad_gate_retained_cells": 5323, "broad_gate_retained_percent": 99.662984459839, "median_nCount_RNA": 3233, "median_nFeature_RNA": 1629, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "DMD_1", "gsm": "GSM8779835", "condition": "DMD", "raw_cells": 3368, "broad_gate_retained_cells": 3368, "broad_gate_retained_percent": 100, "median_nCount_RNA": 1874.5, "median_nFeature_RNA": 1225, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "DMD_2", "gsm": "GSM8779836", "condition": "DMD", "raw_cells": 3063, "broad_gate_retained_cells": 3062, "broad_gate_retained_percent": 99.9673522690173, "median_nCount_RNA": 4742, "median_nFeature_RNA": 2235, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" }, { "sample_id": "DMD_3", "gsm": "GSM8779837", "condition": "DMD", "raw_cells": 6116, "broad_gate_retained_cells": 6116, "broad_gate_retained_percent": 100, "median_nCount_RNA": 2965.5, "median_nFeature_RNA": 1625, "matrix_qc_status": "PASS", "normal_2_flag": false, "context_role": "DESCRIPTIVE_CONTEXT_ALLOWED" } ], "module_summaries": [ { "module_key": "FAP_fibroblast:FAP_ECM_fibrosis", "coarse_celltype": "FAP_fibroblast", "module": "FAP_ECM_fibrosis", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": 0.7303446173552561, "mean_score_excluding_normal_2": 0.8010958180284597 }, "BMD": { "n_samples": 3, "mean_score": 0.5997613247666823, "mean_score_excluding_normal_2": 0.5997613247666823 }, "DMD": { "n_samples": 3, "mean_score": 0.9276443877029129, "mean_score_excluding_normal_2": 0.9276443877029129 } } }, { "module_key": "FAP_fibroblast:regeneration_stress", "coarse_celltype": "FAP_fibroblast", "module": "regeneration_stress", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": -0.11551122864781496, "mean_score_excluding_normal_2": -0.1281570164578581 }, "BMD": { "n_samples": 3, "mean_score": 0.16220826905509114, "mean_score_excluding_normal_2": 0.16220826905509114 }, "DMD": { "n_samples": 3, "mean_score": -0.08065003169824865, "mean_score_excluding_normal_2": -0.08065003169824865 } } }, { "module_key": "macrophage_monocyte:macrophage_inflammatory_state", "coarse_celltype": "macrophage_monocyte", "module": "macrophage_inflammatory_state", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": 0.13902916088877965, "mean_score_excluding_normal_2": 0.16961853707350785 }, "BMD": { "n_samples": 3, "mean_score": 0.13077289360593924, "mean_score_excluding_normal_2": 0.13077289360593924 }, "DMD": { "n_samples": 3, "mean_score": 0.176978445776667, "mean_score_excluding_normal_2": 0.176978445776667 } } }, { "module_key": "myonuclei_contractile:oxidative_mito_score", "coarse_celltype": "myonuclei_contractile", "module": "oxidative_mito_score", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": 0.03236443529573396, "mean_score_excluding_normal_2": 0.0366094612297601 }, "BMD": { "n_samples": 3, "mean_score": 0.10043015513407798, "mean_score_excluding_normal_2": 0.10043015513407798 }, "DMD": { "n_samples": 3, "mean_score": 0.019002132568738755, "mean_score_excluding_normal_2": 0.019002132568738755 } } }, { "module_key": "myonuclei_contractile:regeneration_stress", "coarse_celltype": "myonuclei_contractile", "module": "regeneration_stress", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": 0.2111612861828978, "mean_score_excluding_normal_2": 0.22544277678414126 }, "BMD": { "n_samples": 3, "mean_score": 0.370723268869068, "mean_score_excluding_normal_2": 0.370723268869068 }, "DMD": { "n_samples": 3, "mean_score": 0.3963536170586053, "mean_score_excluding_normal_2": 0.3963536170586053 } } }, { "module_key": "satellite_myogenic:regeneration_stress", "coarse_celltype": "satellite_myogenic", "module": "regeneration_stress", "n_sample_rows": 11, "normal_2_excluded_from_sensitivity": true, "by_condition": { "Normal": { "n_samples": 5, "mean_score": 0.0780242622801686, "mean_score_excluding_normal_2": 0.07550394697555038 }, "BMD": { "n_samples": 3, "mean_score": 0.33442652446550153, "mean_score_excluding_normal_2": 0.33442652446550153 }, "DMD": { "n_samples": 3, "mean_score": 0.10357441450014611, "mean_score_excluding_normal_2": 0.10357441450014611 } } } ], "stable_module_keys": [ "FAP_fibroblast:FAP_ECM_fibrosis", "FAP_fibroblast:regeneration_stress", "macrophage_monocyte:macrophage_inflammatory_state", "myonuclei_contractile:oxidative_mito_score", "myonuclei_contractile:regeneration_stress", "satellite_myogenic:regeneration_stress" ], "unstable_modules_excluded": [ "macrophage_monocyte:TLR2_NOD2_sensing" ], "candidate_context_triage": { "rows": 21, "mapped_candidates": [ "ADAM10", "CPEB1" ], "not_mapped_candidates": [ "CALR", "MPHOSPH6", "ZNF236", "EPS8L1", "INTS13", "RAC3", "DNM1", 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"normal_2_sensitivity_predeclared": true, "formal_ambient_closed": false, "independent_doublet_sensitivity_closed": true, "independent_annotation_disagreement_audit_closed": true, "inherited_labels_overwritten": false, "author_exact_reprocessing_closed": false, "disease_effect_testing_authorized": false, "model_training_labels_allowed": false, "direct_dmd_perturbation_truth": false }, "source_artifacts": { "stable_input": { "role": "stable_input", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/stable_module_context_input/gse288958_stable_module_context_input.tsv", "state": "CONTEXT_INPUT_CHECKSUMMED", "size_bytes": 10506, "sha256": "c6dfd032b994fdf0a0d17e2a257566fd563dc01e746023cd6121799e89dfc93a" }, "stable_manifest": { "role": "stable_manifest", "path": "neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/stable_module_context_input/gse288958_stable_module_context_input.json", "state": 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"neuromuscular_virtual_cell/data/external/GSE288958/metadata/existing_reference_preflight/qc_context_gate/gse288958_qc_context_gate_by_sample.tsv", "state": "CONTEXT_INPUT_CHECKSUMMED", "size_bytes": 2627, "sha256": "075b8491e1c650cf7b6356eb22e6f1068d7f93e7295bc66ae84253d4b5bde41c" } }, "reference_audit": { "audit_id": "GSE288958:REFERENCE-AUDIT:20260909:1", "supersedes_partial_audit_level": "PARTIAL_ANNOTATION_AND_SENSITIVITY_AUDIT", "api_route": "/resource/api/v1.1/gse288958_reference_audit.json", "web_route": "/resource/gse288958-audit/", "independent_doublet_candidates": 1579, "independent_doublet_fraction": 0.026662388977069334, "independent_annotation_resolved_cells": 58912, "independent_annotation_unresolved_cells": 310, "independent_annotation_concordance_fraction_resolved": 0.7588606735469854 }, "claim_boundary": "This object supports bounded descriptive, sample-aware module context with predeclared Normal_2, independent Scrublet and annotation-disagreement sensitivities. It does not support disease-effect p-values, causal inference, model-training labels, therapeutic efficacy, author-exact reprocessing, formal ambient-RNA clearance or direct DMD perturbation truth.", "next_gate": "Use the bounded context object with all three sensitivity layers. Unfiltered droplets are needed only for ambient-RNA closure, and exact author artifacts are needed only before an author-exact reprocessing claim.", "markdown": "# GSE288958 sample-aware context object\n\n- Object ID: `CONTEXT:GSE288958:SAMPLE_AWARE_MODULE:1.1`\n- Status: **CITABLE_BOUNDED_REFERENCE_CONTEXT_INDEPENDENT_AUDITS_COMPLETE**\n- Checked: 2026-08-12T18:15:46+0800\n\n## Scope\n\nDMD/BMD/control muscle sample-aware context reuse from the existing processed reference. The inferential unit is **independent biopsy/sample; cells are nested observations and not independent disease replicates**.\n\n## Denominators\n\n- Raw matrix inventory: **61,189** cells\n- Read-only broad QC gate: **59,237** cells\n- Pilot RDS: **59,222** cells\n- Raw minus pilot: **1,967** cells\n\n## Context policy\n\n- Stable modules retained: **6**\n- Unstable module excluded: `macrophage_monocyte:TLR2_NOD2_sensing`\n- Candidate context-only alignments: **ADAM10, CPEB1**\n- Normal_2 remains in all-sample summaries and is excluded only in the predeclared sensitivity rerun.\n- Donor-wise Scrublet and the independent annotation-disagreement audit are linked through `GSE288958:REFERENCE-AUDIT:20260909:1`.\n\n## Claim boundary\n\nThis object supports bounded descriptive, sample-aware module context with predeclared Normal_2, independent Scrublet and annotation-disagreement sensitivities. It does not support disease-effect p-values, causal inference, model-training labels, therapeutic efficacy, author-exact reprocessing, formal ambient-RNA clearance or direct DMD perturbation truth.\n\nDirect DMD candidate perturbation truth remains **0/21**.\n", "stable_module_tsv": "sample_id\tcondition\tcoarse_celltype\tmodule\tmodule_key\tmodule_score\tnormal2_flag\tcontext_use\ttraining_label_allowed\tdisease_effect_testing_authorized\tdirect_perturbation_truth\r\nBMD_1\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.697541609496592\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.149251596038956\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.512636713792647\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t0.0635312010319975\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.589105651010808\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t0.572345202172232\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.979079930863779\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.198052062204519\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.963292251703173\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.00795765934277582\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.840560980541787\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0359403735474511\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.421827852262449\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.159945314885268\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.447339814662442\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0649280774076423\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t0.41134752311047\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.120789978819349\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t1.06137129820314\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.0716617937191094\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tFAP_fibroblast\tFAP_ECM_fibrosis\tFAP_fibroblast:FAP_ECM_fibrosis\t1.30983659853778\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tFAP_fibroblast\tregeneration_stress\tFAP_fibroblast:regeneration_stress\t-0.160230978407706\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0867922498375757\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.153577559873763\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.151948871106479\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.153315732553065\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.231436472779371\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.146183131997565\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0663036065923441\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0166716561498669\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.0561172006942313\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.234431069630272\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmacrophage_monocyte\tmacrophage_inflammatory_state\tmacrophage_monocyte:macrophage_inflammatory_state\t0.321622271377184\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0188623398694717\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.308383934627271\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0328386595997632\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.278331469545741\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.249589465932999\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.525454402434192\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t-0.00628796229747893\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.299391623974486\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0510268107781476\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.470647324724108\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0122675492255476\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.419021902477222\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0791485232175506\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.120125490686228\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0153843315596294\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.154035323777924\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t-0.0236779848498501\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.341196058289937\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0769194181761811\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.171232292027875\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmyonuclei_contractile\toxidative_mito_score\tmyonuclei_contractile:oxidative_mito_score\t0.0140478883751588\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tmyonuclei_contractile\tregeneration_stress\tmyonuclei_contractile:regeneration_stress\t0.269217266132525\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_1\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0205732997710225\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_2\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.227225358302042\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nBMD_3\tBMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.75548091532344\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_1\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t-0.00509484809381969\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_2\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.140290124444811\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nDMD_3\tDMD\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.175527967149447\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_1\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0237234583751645\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_2\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0881055234986414\tTrue\tSENSITIVITY_FLAGGED\tFalse\tFalse\tFalse\r\nNormal_3\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0166868187557854\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_4\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.236239919509336\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\nNormal_5\tNormal\tsatellite_myogenic\tregeneration_stress\tsatellite_myogenic:regeneration_stress\t0.0253655912619156\tFalse\tDESCRIPTIVE_CONTEXT\tFalse\tFalse\tFalse\r\n", "candidate_triage_tsv": "gene\texperimental_rank\tpriority_tier\texperimental_role\tmechanism_axis\tcandidate_context_decision\tcontext_overlay_status\tsupporting_context_modules\tcontext_celltypes\tall_samples_delta\tnormal2_excluded_delta\tdirection_stability\tstable_module_count\tstable_module_sample_rows\tstable_module_sample_count\tstable_module_flagged_samples\tqc_context_gate_state\tnormal2_sensitivity_required\ttraining_label_allowed\tdisease_effect_testing_authorized\tdirect_dmd_perturbation_truth\texperimental_rank_preserved\tcandidate_score_changed\texternal_context_evidence_scope\tcandidate_claim_ceiling\tmodel_output_changed\tmapping_rationale\texcluded_unstable_context\r\nADAM10\t1\tA\tprimary_rescue\tmembrane shedding / Notch / adhesion\tSUPPORTIVE_STABLE_MODULE_CONTEXT\tSUPPORTIVE_CONTEXT_ALIGNMENT_NOT_GENE_VALIDATED\tsatellite_myogenic:regeneration_stress\tsatellite_myogenic\tsatellite_myogenic:regeneration_stress=0.025550\tsatellite_myogenic:regeneration_stress=0.028070\tPRESERVED_AFTER_NORMAL_2_EXCLUSION\t1\t11\t11\tNormal_2\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tL2_CONTEXT_TRIAGE_ONLY\tFALSE\tExisting ranking links ADAM10 to muscle Notch/satellite-cell biology; the reference satellite regeneration-stress module is direction-stable.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nCALR\t2\tA\tprimary_rescue\tER proteostasis / calcium handling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nMPHOSPH6\t3\tA\tprimary_rescue\tnuclear RNA exosome / RNA surveillance\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZNF236\t4\tB\thigh_information_contrast\ttranscriptional phenotype / candidate ribosome-biogenesis regulator\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nCPEB1\t5\tB\tmuscle_mechanism_contrast\tcytoplasmic polyadenylation / MYOD1 translation\tSUPPORTIVE_STABLE_MODULE_CONTEXT\tSUPPORTIVE_CONTEXT_ALIGNMENT_NOT_GENE_VALIDATED\tsatellite_myogenic:regeneration_stress\tsatellite_myogenic\tsatellite_myogenic:regeneration_stress=0.025550\tsatellite_myogenic:regeneration_stress=0.028070\tPRESERVED_AFTER_NORMAL_2_EXCLUSION\t1\t11\t11\tNormal_2\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tL2_CONTEXT_TRIAGE_ONLY\tFALSE\tExisting ranking links CPEB1 to MYOD1 translation and muscle-regeneration biology; the reference satellite regeneration-stress module is direction-stable.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nEPS8L1\t6\tB\ttransfer_contrast\tRAC-linked actin remodeling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nINTS13\t7\tB\tdiscordance_contrast\tIntegrator enhancer module / lineage transcription\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRAC3\t8\tB\tcytoskeleton_contrast\tRho-family actin / adhesion signaling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDNM1\t9\tC\texploratory\tdynamin-dependent membrane fission\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nGFOD2\t10\tC\texploratory\tpoorly characterized oxidoreductase-like protein\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nMON1A\t11\tC\texploratory\tRab7 activation / endolysosomal maturation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nEHMT2\t12\tC\tmechanism_negative_control\tH3K9 methylation / chromatin repression\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDDX19B\t13\tD\tfailure_mode_calibration\tmRNA export termination / RNA remodeling\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nNAGLU\t14\tD\tfailure_mode_calibration\tlysosomal heparan-sulfate degradation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nWDR4\t15\tD\tfailure_mode_calibration\tMETTL1-WDR4 tRNA m7G methylation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRNF8\t16\tD\tfailure_mode_calibration\tDNA-damage histone ubiquitylation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nRNASEH2C\t17\tD\tfailure_mode_calibration\tRNase H2 / ribonucleotide and R-loop removal\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZFP69B\t18\tE\tlow_priority_calibration\tpoorly characterized zinc-finger regulation\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nDNAAF3\t19\tE\tlow_priority_calibration\taxonemal-dynein preassembly\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nLMO2\t20\tE\tsafety_calibration\thematopoietic / endothelial transcriptional cofactor\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\nZNF133\t21\tE\thistorical_negative_control\tKRAB zinc-finger transcriptional repression\tNO_DIRECT_STABLE_MODULE_MAPPING\tNOT_MAPPED_NO_DIRECT_GENE_MODULE_LINK\t\t\t\t\tNOT_ASSESSED\t0\t0\t0\t\tDESCRIPTIVE_ONLY_NORMAL_2_SENSITIVITY\tTRUE\tFALSE\tFALSE\tFALSE\tTRUE\tFALSE\tMODULE_LEVEL_CONTEXT_ONLY\tNO_GENE_LEVEL_CONTEXT_CLAIM\tFALSE\tNo direct candidate-to-reference-module link was documented in the existing ranking evidence; no context support is assigned.\tmacrophage_monocyte:TLR2_NOD2_sensing\r\n" }, "top_line_decision": "NMD-VCell should invest next in source recovery, donor-resolved data objects and one baseline-first public benchmark adapter—not in another unvalidated DMD predictor label.", "claim_boundary": "External models, datasets and platform practices are opportunities or design references. They are not inherited evidence, local execution results or validated DMD predictions." }