NMD-VCell Neuromuscular Virtual Cell Research Platform Module: Design · Evidence → perturbation → experiment → outcome NMD = neuromuscular disorders
For Reviewers Current Release

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

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

GFOD2 Study Card

Truth-generation Study Card

SC:v1.2.0-measured-dmd-evidence:GFOD2:1.5-DRAFTDRAFT

GFOD2

evidence import audit Provisional hold · external report not yet audited

Does the author-reported external evidence for GFOD2 meet provenance, context, independence and negative-evidence criteria?

Registration completeness38%
Missing before registration
  • source accession
  • numeric effect and interval
  • denominator and exclusion flow
  • code/provenance reproducibility
  • negative-evidence rule

Decision summary

GFOD2 is ready for a bounded next step, not a DMD response claim.

Does the author-reported external evidence for GFOD2 meet provenance, context, independence and negative-evidence criteria?

What we know
observed same context perturbation
What remains uncertain
GAP-09 External quantitative evidence has not been imported and audited
Experiment entry state
Evidence audit required before experimental escalation
Next action
Provisional hold · external report not yet audited
Lifecycle track
Generate new truth. A prediction is not required for this study.
First fields to close
  • source accession
  • numeric effect and interval
  • denominator and exclusion flow
  • code/provenance reproducibility
  • negative-evidence rule
Continue the designInspect the evidence

Study Freeze Gate

Complete the required design fields before creating a review-ready frozen dossier.

Readiness: 38% · 5 required fields remain open.

Complete required fields

Freezing creates an immutable, checksum-bound Study dossier. External registration remains a separate authority action.

Research object trace

GENE:v1.2.0-measured-dmd-evidence:GFOD2 → CMP-20260726-A04D03258188 → PLN:v1.2.0-measured-dmd-evidence:GFOD2:1.0-DRAFT → SC:v1.2.0-measured-dmd-evidence:GFOD2:1.5-DRAFT → OUT:v1.2.0-measured-dmd-evidence:GFOD2:PENDING

Traceability only; object links do not register a prediction or measured DMD outcome.

SuggestedSelectedFrozenMeasuredCurrent protocol values are suggestions until experimental authority selects and freezes them.

Study Card visual summary

Frozen evidence and registration route

This multi-panel view turns the frozen Study Card fields into a visual audit of what is known, what is missing and what must be registered next.

BoundaryDescriptive frozen evidence snapshot only; no score, rank, cluster, prediction claim or intervention recommendation is generated.
Registration readiness 38% 5 open fields
Current supported level L2 observed same context perturbation Observed evidence ceiling in this record
Highest assessed context L2 observed same context perturbation Assessment does not imply support
Target closure layer L4 DMD functional validation required
DMD source agreement 50% 2/4 sources · conflicted
Muscle expression 2.95 TPM above 1 TPM context flag
a

Frozen evidence route

  1. L1Resource recordHGNC-resolved typed research object
  2. L2Observed HepG2 perturbation127 observed cells
  3. L3aExternal context screennot assessed
  4. L3bIndependent perturbation replicationsame-perturbation replication absent
  5. L4DMD muscle functional validationDMD-relevant functional validation absent
  6. REGRegistered Study Card5 open fields before registration
b

Bioinformatics result snapshot

Legacy integrated DMD priorup
Source agreement50%
Skeletal-muscle TPM2.95
External screennot assessed
Dependency cautionnot flagged
DepMap effect-0.077
c

Evidence-to-experiment route

Context

External-evidence audit only; no new biological escalation until the quantitative import is complete.

Perturb

None. This card imports and audits an existing evidence object.

Endpoint

Completeness, reproducibility and claim-ceiling classification of the imported quantitative result.

Infer

Required import field: preserve the source study’s declared inferential unit exactly.

Model

Reproduce the source model exactly when code and inputs permit; otherwise classify as not reproducible.

d

Registration gap map

  • source accession
  • numeric effect and interval
  • denominator and exclusion flow
  • code/provenance reproducibility
  • negative-evidence rule

These bars are field-state indicators only. They do not create a target score, rank, cluster or prediction claim.

Field state · Suggested

Design options for experimental review

Biological context

External-evidence audit only; no new biological escalation until the quantitative import is complete.

Perturbation modality

None. This card imports and audits an existing evidence object.

Primary endpoint

Completeness, reproducibility and claim-ceiling classification of the imported quantitative result.

Primary estimand

Imported effect estimate with its uncertainty, denominator and exact contrast; no reconstructed estimate is accepted without provenance.

Inferential unit

Required import field: preserve the source study’s declared inferential unit exactly.

Statistical model

Reproduce the source model exactly when code and inputs permit; otherwise classify as not reproducible.

Decision-blocking gap

GAP-09 External quantitative evidence has not been imported and audited

Highest missing evidence layer

L4 dmd functional validation

GAP-02 independent muscle-context perturbation; GAP-03 DMD-relevant functional validation; GAP-07 independent replication

Perturbation-direction rationale

Current selection: not applicable

No new perturbation direction is nominated by an evidence-import audit.

Allowed registered hypotheses: not applicable.

Comparator and controls

  • Dataset accession and source owner.
  • Raw/processed availability.
  • Target mapping and assay context.
  • Primary endpoint, effect size and uncertainty.
  • Independent reproduction and import acceptance criteria.

Secondary endpoints

  • Provenance completeness.
  • Context match.
  • Negligible-effect interpretation.
  • Independent reproduction status.

State-transition extension

Mechanism hypothesis and registered time axis

Scientific object: perturbation × cell state × disease context × time × phenotype

Required before registration: state the proposed early molecular mediator, the expected cell-state transition and the downstream functional consequence.

6–12 hearly molecular or signalling response

planning default requires assay calibration

24–48 hregulatory program and cell-state transition

planning default requires assay calibration

4–7 ddifferentiation and functional phenotype

planning default requires assay calibration

Cell context fields

Required before registration: healthy, DMD or isogenic corrected. Required before registration: proliferating myoblast, early differentiation, fusion or maturing myotube. Required before registration; preserve donor-specific estimates.

Cell–cell consequence

Current status: not assessed. Future levels: conditioned medium; two-cell co-culture; three-dimensional muscle model; spatial perturbation model.

Blocking factors

  • Source study.
  • Assay batch.
  • Biological context.
  • Analysis version.

Assay QC thresholds

  • Accession resolvable.
  • Raw or sufficient processed data available.
  • Target mapping exact.
  • Effect, interval and denominator present.
  • Code/provenance sufficient for reproduction.

Evidence-import requirements

  • Source accession and owner.
  • Raw and processed data availability.
  • Exact denominator and exclusion flow.
  • Effect estimate, interval and primary contrast.
  • Original allocation and inferential unit.
  • Preregistration status.
  • Code and environment reproducibility.
  • Reagent and donor replication.
  • Negative-result definition.
  • Selective-reporting assessment.

Prospective planning fields are intentionally not applied: minimally_important_effect, negligible_effect_margin, suggested_sample_size_range, randomisation_unit.

Multiplicity and missing data

Preserve the source family and correction; do not reinterpret an isolated P value.

Define exclusions before unblinding; report all missing units and reasons; do not single-impute primary outcomes without a prespecified sensitivity analysis.

Replication rules

Not applicable unless the imported study reports multiple reagents; if so, preserve reagent-specific results.

Record whether the source result replicates across donors/samples; absence is a limitation, not a negative result.

Stop rules

  • Stop or classify as infeasible if a required numeric QC threshold fails.
  • Do not interpret a nonsignificant result as no material effect without a negligible-effect interval.
  • Do not change canonical candidate status automatically; require governed review.
Time and cost2–10 working days after complete source delivery; planning estimate only. Institution- and assay-dependent; obtain a local itemised quote before registration.
Preregistration statusdraft requires source accession denominator contrast and reproducibility audit
Lifecycle ruleThis draft is editable. Registration requires a timestamp and checksum; a registered revision is immutable and any correction must supersede it.
Escalation ruleRetain, release or formally change the hold only after provenance, independence and negative-evidence gates are audited.
Evidence transitionAuthor report pending import → audited evidence object → governed status decision.

Version history

Study Card 1.4 → 1.5

Field groupChangeScientific effect
Object identityCard schema and object version advanced to 1.5.Traceability only
State-transition designCell context, timepoint roles, mechanism hypothesis and cell–cell consequence fields added.Design scaffold expanded
Frozen evidenceNo supporting evidence, evidence level or outcome was added.Unchanged

This is a draft-to-draft schema revision, not a registered-study amendment and not an evidence upgrade.

Data-release planRelease the frozen card, protocol identifiers, analysis code, complete denominators and results irrespective of direction; never overwrite the registered card.
Boundary: This Study Card is an evidence-gated design scaffold, not a protocol, power calculation, safety claim, prediction or therapeutic recommendation.