NMD-VCell Neuromuscular Virtual Cell Research Platform Module: Data · Evidence → perturbation → experiment → outcome NMD = neuromuscular disorders

Release 2026.08DMD context observedDMD candidate-conditioned prediction not yet eligible

View scientific status
Evidence freeze: 3 August 2026 Resource: v1.2.0-measured-dmd-evidence Schema: 1.1 Open release status →

Data Universe · scientific inventory workbench

Know what exists, what qualifies, and what is still missing.

Storage presence, analysis coverage, public mapping and prediction qualification answer different scientific questions. This page preserves their real units and lets you inspect one governed object at a time.

Summary matrix

One platform, four non-interchangeable questions.

Each row declares the object type, counting unit and inclusion rule before showing a value.

Open qualified Dataset Cards →
Scientific questionObject typeCounting unitInclusion ruleCurrent state
What is stored?Source collectionFamilyPresent in audited workspace or governed /share inventory12 workspace + 80 server families
What has been analyzed?Result collectionAnalysis familyDerived output family exists; not an independent validation65 workspace + 66 server families
What is publicly mapped?Inventory record / API objectPublic summary or fileReleased through a stable public route126 inventory records · 712 API files
What qualifies a prediction?Dataset Card + ModelRun + OutcomeTask-qualified evidence chainMatched context, frozen task, baseline gate and measured outcomeNot yet qualified for DMD candidate response

5 task-audited datasets126 public inventory records92+ stored family-level collections

Data value map

What can this data answer now, and where should it go next?

The inventory is useful when each data family is routed to the right scientific task. This map turns storage into decision flow without pretending that coverage is calibration.

Ask a bounded virtual-cell question →
Disease context 12 workspace source families + 80 server families
Can answer now
Which disease, donor, tissue and cell-state contexts are represented well enough to frame a DMD question.
Cannot answer alone
Whether one candidate perturbation changes a DMD muscle outcome.
Model or experiment handoff
Open Disease Atlas or Cell Browser before selecting a perturbation.
Open route →
Perturbation substrate 5 task-audited Dataset Cards
Can answer now
Which observed perturbation substrates and contextual screens are reusable for baseline, transfer or assay design.
Cannot answer alone
A calibrated DMD rescue, toxicity or fusion prediction without matched disease-context outcomes.
Model or experiment handoff
Open Dataset Cards, then ask the target in Virtual Cell.
Open route →
Model execution 6 registered ModelRuns + 2 model asset families
Can answer now
Which model runs executed, which benchmarks are permanent controls and which task gates failed or remain locked.
Cannot answer alone
A disease-conditioned counterfactual when the required outcome edge is absent.
Model or experiment handoff
Open ModelRun Registry or Benchmark Center before interpreting model-like outputs.
Open route →
Truth generation Matched DMD candidate outcomes remain the decision-critical missing edge
Can answer now
Which experiment would convert an evidence gap into a reusable outcome object.
Cannot answer alone
A positive or negative biological effect before the registered study exists.
Model or experiment handoff
Use Planner or Study Cards to freeze assay, controls, endpoint and decision rule.
Open route →

Shared reading grammar

Evidence metadata fields—never one confidence score.

Every state uses text plus a shape or border. Missing evidence and a equivalent-null result are different states.

Origin Observed Computational Missing
Context relation Target context Same tissue Locus correction External cell
Unit structure Donor / line Culture Pathway Not estimable
Lifecycle Draft Frozen Registered Released
Outcome / absence Supportive Measured null Inconclusive Not measured

Scientific datasets · default view

Start with five datasets audited for a defined computational role.

Each Dataset Card states context, task, units and claim boundary. Derived analyses and storage inventory remain available below for Audit use.

Open all Dataset Cards →
Perturbation substrateNMD-VCell HepG2 CRISPRi

Same-assay response substrate and permanent baseline context.

Open Dataset Card →
DMD correctionGSE272233

Patient-derived and corrected cellular reference with biological units preserved.

Open Dataset Card →
Human myoblast functionGSE293514

Healthy-myoblast fusion perturbation evidence; contextual, not DMD replication.

Open Dataset Card →
Myogenic trajectoryGSE52529

Unperturbed human differentiation reference across physical time.

Open Dataset Card →
Combination calibrationGSE133344

Non-muscle CRISPRa method calibration; no inherited DMD claim.

Open Dataset Card →
Technical inventory — Audit · 126 governed records

Table + inspector

126 governed inventory records

Select a row to inspect what the object proves, what it cannot prove and where its public object lives.

Showing all 126 mapped assets.

ObjectLayerDiseaseModalityStateScale
sourceNon-muscle method calibrationK562AVAILABLE287 perturbations; 112 singles; 132 pairs
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceDuchenne muscular dystrophyPatient-derived and corrected cellular modelsAVAILABLE21 samples; 3 per reported group
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceMuscle context; not DMD rescueHuman myoblastAVAILABLE7,197 screen genes; 250 hits; 125 individually validated genes
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceNon-disease trajectory referencePrimary human skeletal myoblastAVAILABLE271 cells
sourceDMDprocessed biological dataAVAILABLEdirectory-level family
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceMulti-contextprocessed biological dataAVAILABLEdirectory-level family
sourceREFERENCEtranscript_to_hgnc_symbol_mappingAVAILABLE1 registered source files
sourceFSHDpatient_myotube_single_nucleus_expression · sample_and_series_metadataAVAILABLE2 registered source files
sourceFSHDdux4_induction_timecourse_raw_counts · dux4_induction_timecourse_tpmAVAILABLE3 registered source files
sourceFSHDmembrane_repair_ferroptosis_file_registry · sample_and_series_metadataAVAILABLE2 registered source files
sourceDM1isogenic_repeat_state_expression · isogenic_repeat_state_differential_expressionAVAILABLE8 registered source files
sourceDM1patient_muscle_raw_counts · patient_muscle_sample_orderAVAILABLE4 registered source files
sourceSMAspinal_organoid_disease_and_aso_rescue_counts · sample_and_series_metadataAVAILABLE2 registered source files
sourceSMAspinal_organoid_single_cell_file_registry · sample_and_series_metadataAVAILABLE2 registered source files
sourceSMAtreated_patient_muscle_gene_counts · treated_patient_muscle_gene_tpmAVAILABLE3 registered source files
sourceSMAmotor_neuron_smn_loss_differential_expression · induced_neuron_smn_loss_differential_expressionAVAILABLE3 registered source files
analysisCross-contextderived analysisANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisCross-contextperturbation / target analysisANALYSIS AVAILABLEresult family
analysisCross-contextspatial / representationANALYSIS AVAILABLEresult family
analysisCross-contextspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisDMDperturbation / target analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisCross-contextderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisDMDspatial / representationANALYSIS AVAILABLEresult family
analysisCross-contextderived analysisANALYSIS AVAILABLEresult family
analysisCross-contextderived analysisANALYSIS AVAILABLEresult family
analysisMulti-diseasederived analysisANALYSIS AVAILABLEresult family
analysisMulti-diseasederived analysisANALYSIS AVAILABLEresult family
analysisDMDderived analysisANALYSIS AVAILABLEresult family
analysisCross-contextderived analysisANALYSIS AVAILABLEresult family
modelCross-contextmodel code / checkpointMODEL ASSET AVAILABLE79 files across 2 model families
modelCross-contextmodel code / checkpointMODEL ASSET AVAILABLE79 files across 2 model families
publicationMulti-diseasemanuscript · figures · tables · evidence-governance schemaCURATED WORKING NOT SUBMISSION READY6 main figures (36 files) · 31 supplementary figures (114 files) · 44 tables
apiMulti-diseaseHTML · JSON · TSV · schemasPUBLISHED669 API files
missingDMDplanned molecular + functional outcomesDECISION CRITICAL GAPNo governed candidate has matched DMD outcome yet
serverDMDsingle-cell · pseudobulkSERVER AVAILABLEannotated objects and cell-type differential results
serverDMDsingle-cell · spatial · NicheNetSERVER AVAILABLEstate-resolved and cell-communication analyses
serverDMDcross-species h5adSERVER AVAILABLESATURN and TranscriptFormer-ready counts
serverCross-contextSTATE · baselines · candidate screensSERVER AVAILABLE66 result families and 2,278 result files
serverDMDpatient 10x matricesSERVER AVAILABLEfour own clinical DMD matrices
serverDMDFASTQ · STARsolo · SRASERVER AVAILABLEretained for reproducibility; not required for current site rendering
serverDMDcsvREADY FOR ANALYSIS50M · priority 1
serverDMDcsvREADY FOR ANALYSIS37M · priority 1
serverDMDtsvREADY FOR ANALYSIS6.4M · priority 1
serverDMDcsvREADY FOR ANALYSIS3.7M · priority 1
serverDMDcsvREADY FOR ANALYSIS24M · priority 1
serverDMDcsvREADY FOR ANALYSIS50M · priority 2
serverDMDrdsREADY FOR ANALYSISmany · priority 2
serverDMDcsvREADY FOR ANALYSISmany · priority 2
serverDMDrdsSERVER AVAILABLE2.19G · priority 2
serverDMDrdsSERVER AVAILABLE838M · priority 3
serverDMDh5adREADY FOR ANALYSIS238M · priority 2
serverDMDh5adREADY FOR ANALYSIS179M · priority 2
serverDMDh5adREADY FOR ANALYSIS38M · priority 3
serverDMDh5adREADY FOR ANALYSIS26M · priority 3
serverDMDh5adREADY FOR ANALYSIS70M · priority 3
serverDMDh5adSERVER AVAILABLE21M-688M · priority 3
serverDMDmtx.gzSERVER AVAILABLE1.08G · priority 3
serverDMDtarSERVER AVAILABLE360M · priority 3
serverDMDmtxSERVER AVAILABLE178M · priority 3
serverDMDmtx.gzSERVER AVAILABLE109M · priority 3
serverDMDmtx.gzSERVER AVAILABLE134M · priority 3
serverDMDmtx.gzSERVER AVAILABLE117M · priority 3
serverDMDmtx.gzSERVER AVAILABLE69M · priority 3
serverDMDfastq+starsoloSERVER AVAILABLE197G · priority 4
serverDMDfastq+starsoloSERVER AVAILABLE235G · priority 4
serverDMDsraSERVER AVAILABLE45G · priority 4
serverDMDmtxSERVER AVAILABLE15M · priority 4
serverDMDmtxSERVER AVAILABLE7.6M · priority 4

Why abundant data can coexist with abstention

Coverage and calibration are different questions.

Available: patient disease context, organoids, biopsies, spatial tissue, cross-species objects, observed perturbations, registered ModelRuns and derived pathways.

Not measured yet: matched candidate perturbation outcomes in DMD-relevant muscle with molecular and functional endpoints. This missing calibration edge—not a lack of project data—keeps the disease counterfactual locked.

Public projection contract

Catalog pages now read an approved public field set

122 public metadata records expose only approved catalog fields. 4 controlled clinical records are collapsed to collection-level metadata.