NMD-VCell Neuromuscular Virtual Cell Research Platform Module: Registry · 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 →

Research-object registry

Validate · research-object registry

Choose the scientific job before choosing the lifecycle.

Generate biological truth when the evidence edge is missing. Validate a prediction only after an eligible model can be frozen before outcome access.

Gene objects17,921 released
Comparison objects5 released
Study Cards21 draft
Decision Cards3 open drafts
Stage A protocol1 panel draft
Panel identities assigned24/24
Panel-freeze statusSignoff pending
Scientific program1 released contract
Perturbation network1 Stage B0 object
No-wet-lab evaluation1 released contract
v1 release gate1 released
Prediction readiness1 released gate
Prediction registry1 empty scaffold
Release objectv1.2.0-measured-dmd-evidence

Module meaning contract

Registry · what this module can change

See all eight modules →
Question answeredWhat is draft, frozen, registered, running, measured, released, superseded or intentionally absent?
Scope & evidence unitTwo layers are explicit: the DMD prospective lifecycle and the released four-disease evidence contract.One immutable versioned research object; a missing record is never interpreted as a negative result.
ProducesLifecycle states for comparisons, Study Cards, protocols, ModelRuns, predictions and outcomes, including honest zero states.
Cannot establishThe public registry is read-only; it does not accept uploads, create persistence or promote zero outcomes into validation.

Next handoffContribute a traceable outcome or evidence object, then apply the formal transition rules. Continue →

Product contract · WORKFLOW-OUTCOME-CARD-1.0

Outcome Card: What was registered, measured or failed—and what conclusion changed?

Study identityFrozen prediction when usedMeasured outcomePositive · null · toxic · failedProvenanceEvidence transition

Two prospective lifecycles

Truth generation and prediction validation are different scientific jobs.

A truth-generating experiment creates the evidence needed to train or calibrate a model. A prediction-validation experiment tests an already eligible model prospectively.

Open lifecycle JSON →
Current stageTruth generationStudy design is available now; prediction validation opens after model eligibility.
TRACK-A-TRUTH-GENERATION

Generate new truth

Design and run an experiment that fills a named biological evidence gap and creates ground truth for later model calibration.

01QuestionDEFINEDQUESTION:{disease}:{context}:{target}
02Study designDRAFTSC:{resource_release}:{gene}:{revision}-DRAFT
03RegistrationAWAITING EXPERIMENTAL AUTHORITYSTUDY:{study_id}:{revision}
04ExperimentREADY AFTER REGISTRATIONEXP:{registered_study_id}:{experiment_id}
05OutcomeRETURN TO REGISTRYOUT:{study_id}:{outcome_revision}
06Truth datasetCREATED FROM QUALIFYING OUTCOMESTRUTH:{study_id}:{release}
07Evidence updateAPPLY RELEASED TRANSITION RULESTRANSITION:{outcome_id}:{revision}
08Model calibrationOPTIONAL DOWNSTREAM USEMRUN:{truth_release}:{model_id}

Next action · Resolve the DMD pilot design fields and register the truth-generating study. No prediction is required for this track.

Design truth-generating study
TRACK-B-PREDICTION-VALIDATION

Test a prediction

Freeze an eligible model output before outcome access, then measure prediction error prospectively.

01Eligible ModelRunREQUIREDMRUN:{model_release}:{run_id}
02Frozen predictionREQUIRED BEFORE OUTCOMEPRED:{model_release}:{prediction_id}
03Registered studyREQUIREDSTUDY:{study_id}:{revision}
04ExperimentRUN AFTER FREEZEEXP:{registered_study_id}:{experiment_id}
05OutcomeBLINDED UNTIL RETURNOUT:{prediction_id}:{outcome_revision}
06Prediction errorCOMPUTE AFTER OUTCOMEERROR:{prediction_id}:{outcome_id}
07CalibrationUPDATE WITHOUT OVERWRITINGCAL:{model_id}:{validation_release}
08Model updateNEW IMMUTABLE MODELRUNMRUN:{model_release}:{run_id}

Next action · Enter this track only after a DMD-compatible ModelRun meets the frozen eligibility gate.

Register prediction-validation study
Governance ruleTruth-generation studies require an immutable registered Study before execution but do not require a Prediction. Prediction-validation studies require both an eligible ModelRun and a frozen Prediction before outcome access.

Null, toxic, discordant and inconclusive outcomes are first-class records and are not removed from the lifecycle.

Shared object states

Draft objects are not failed validations.

DRAFTEditable design
REGISTEREDImmutable protocol identity
RUNNINGExecution linked to its Study
MEASUREDOutcome returned
RELEASEDEvidence transition published

Open research decisions

Decision Cards connect uncertainty to a result that can change the record

These cards are editable drafts. They organize a discriminating experiment, an evidence audit and a prospective panel freeze without claiming a winner.

Open the Research Decision Queue → · Open machine-readable cards →

Protocol parent object

DMD Minimum Perturbome Stage A Panel Draft

PROTOCOL:v1.2.0-measured-dmd-evidence:DMD-MIN-PERTURBOME:1.1-PANEL-DRAFT provisionally assigns 14 candidate genes, 10 calibration controls and six prospectively sealed roles. It remains editable until panel signoff, assay calibration, approvals, reagent identities and an immutable Study object are complete. A Prediction object is required only if the study later enters the prediction-validation track.

State authority: PANEL_DRAFT_ASSIGNED_SIGNOFF_PENDING · effective 2026-08-06 · next PANEL_FROZEN_ENDPOINT_FROZEN_READY_FOR_REGISTRATION.

Open Panel Draft · Open protocol JSON · Open project-state JSON

Released examples

Frozen comparisons with rendered results

These objects resolve without a query string or client-side JavaScript. Each preserves inputs, mappings, release identity, checksum, JSON and TSV.

Immutable worked examples; no ranking generated
Object IDPurposeGenesState
CMP-20260726-A04D03258188 Three-gene evidence-gap comparisonZNF133, MON1A, GFOD2 RELEASED
CMP-20260726-311ECF4EC825 Shared-action comparisonZNF133, MON1A RELEASED
CMP-20260726-9EDD5E7C9212 External-context contrastGFOD2, ZFP69B, CPEB1 RELEASED
CMP-20260726-FE0FF0F808F4 Computational-replication queueINTS13, NAGLU, RNF8 RELEASED
CMP-20260726-BF1FA85ADE20 Mixed action and gap comparisonZNF133, WDR4, GFOD2, INTS13 RELEASED

Lifecycle contract

Draft → registered → measured → superseded

DRAFTEditable planning object
REGISTEREDImmutable; timestamp and checksum required
MEASUREDOutcome linked without overwriting prediction
SUPERSEDEDNew revision links to prior object
Current boundary. This static public beta exposes read-only contracts and draft objects. It does not accept uploads or claim registry persistence without an approved storage, identity and governance policy.

Released governance object

PredictionReadiness gate

PREAD:v1.2.0-measured-dmd-evidence:EA-20260817-57 is a released governance object. It states that P0 infrastructure is available, P1 research-use DMD prediction is locked pending independent disease-relevant perturbation validation, and P2 clinical prediction is outside the current release.

Open rendered object · Open JSON

Released scientific contract

State-transition program and DMD Minimum Perturbome

PROGRAM:v1.2.0-measured-dmd-evidence:STATE-TRANSITION:1.0 defines the dual-track scientific program. The no-new-wet-lab pack contributes eleven bounded evaluation modules, including a partial UniPert source-and-identifier feasibility audit; the 24-slot Minimum Perturbome has 14 candidate and 10 control assignments and is awaiting study registration.

Open scientific program · Open no-new-wet-lab pack · Open UniPert feasibility · Open draft pilot · Registered Study registry · Outcome registry

Released observed network

Human Myoblast Perturbation Network · Stage B0

HMPN:v1.2.0-measured-dmd-evidence:EA-20260817-57:STAGE-B0 freezes 92 evidence-typed edges from GSE293514, including 31 exact fusion-screen effects, 17 individual-validation edges and two qualitative grouped CROP-seq state edges. Its 21-candidate audit records 9 assessed genes, 0 fusion hits and 12 genes outside the library. DMD prediction edges remain 0.

Open rendered network · Open network JSON · Download edges

Released publication objects

V1ReleaseGate, ExternalAuthorizationDossier and PredictionRegistry

V1GATE:v1.2.0-measured-dmd-evidence:EA-20260817-57 records formal database-paper readiness without authorizing formal v1.0. AUTHD:v1.2.0-measured-dmd-evidence:EA-20260817-57 records the DOI/licence/maintainer dossier that remains pending external input. PREG:v1.2.0-measured-dmd-evidence:EA-20260817-57 records the empty prospective prediction registry; no prediction or measured-outcome record has been registered yet.

Open v1 gate · Open authorization dossier · Open prediction registry

Governed hypotheses

All 21 Study Cards remain drafts

Draft Study Cards; alphabetical, not ranked
Object IDTypeGeneStateCurrent action
SC:v1.2.0-measured-dmd-evidence:ADAM10:1.5-DRAFT StudyCardADAM10DRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:CALR:1.5-DRAFT StudyCardCALRDRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:CPEB1:1.5-DRAFT StudyCardCPEB1DRAFT Verify expression
SC:v1.2.0-measured-dmd-evidence:DDX19B:1.5-DRAFT StudyCardDDX19BDRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:DNAAF3:1.5-DRAFT StudyCardDNAAF3DRAFT Verify expression
SC:v1.2.0-measured-dmd-evidence:DNM1:1.5-DRAFT StudyCardDNM1DRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:EHMT2:1.5-DRAFT StudyCardEHMT2DRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:EPS8L1:1.5-DRAFT StudyCardEPS8L1DRAFT Verify expression
SC:v1.2.0-measured-dmd-evidence:GFOD2:1.5-DRAFT StudyCardGFOD2DRAFT Provisional hold · external report not yet audited
SC:v1.2.0-measured-dmd-evidence:INTS13:1.5-DRAFT StudyCardINTS13DRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:LMO2:1.5-DRAFT StudyCardLMO2DRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:MON1A:1.5-DRAFT StudyCardMON1ADRAFT Muscle-context assay
SC:v1.2.0-measured-dmd-evidence:MPHOSPH6:1.5-DRAFT StudyCardMPHOSPH6DRAFT Computational replication
SC:v1.2.0-measured-dmd-evidence:NAGLU:1.5-DRAFT StudyCardNAGLUDRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:RAC3:1.5-DRAFT StudyCardRAC3DRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:RNASEH2C:1.5-DRAFT StudyCardRNASEH2CDRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:RNF8:1.5-DRAFT StudyCardRNF8DRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:WDR4:1.5-DRAFT StudyCardWDR4DRAFT Risk/context review
SC:v1.2.0-measured-dmd-evidence:ZFP69B:1.5-DRAFT StudyCardZFP69BDRAFT Verify expression
SC:v1.2.0-measured-dmd-evidence:ZNF133:1.5-DRAFT StudyCardZNF133DRAFT Muscle-context assay
SC:v1.2.0-measured-dmd-evidence:ZNF236:1.5-DRAFT StudyCardZNF236DRAFT Risk/context review

Machine contract

Strict object schemas, transition rules and null semantics are published separately from the frozen schema 1.1 gene API.

Manifest · Schemas · Registry JSON

Operational readiness

Reproducibility, maintenance, structured-metadata and accessibility targets are explicit objects, including unresolved institutional gates.

Reproducibility · Maintenance · Accessibility