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

Evidence Release 2026.08DMD context observedDMD candidate-conditioned prediction locked

View scientific status
Evidence freeze: 3 August 2026 P59 hold · scorer failure retained · no target score NAR working package · 6 main + 31 supplementary figures Resource: v1.2.0-measured-dmd-evidence Schema: 1.1 Open platform state → Open Trust Center → Open evidence dashboard → Open claim registry → Open release status →

Downloads

Module meaning contract

Data & API · what this module can change

See all eight modules →
Question answeredWhich exact bytes, schema, identifier, checksum and release boundary support a displayed result?
Scope & evidence unitCovers the DMD workbench and the additive four-disease v2 evidence contract through versioned files and static APIs.One versioned file or API object with a declared schema, provenance path and checksum identity.
ProducesJSON, TSV, schemas, manifests, checksums, release bundles and a portable RO-Crate contract.
Cannot establishMachine readability or file availability does not expand biological claims; hosting exclusions remain declared rather than silently omitted.

Next handoffVerify the object, then return to the module whose scientific question it supports. Continue →

Governed discovery · V201 production content

Find current, publication and historical objects without treating the directory as authority.

This navigator exposes 19 governed entry objects. The full file ledger remains available for audit, but package membership and current status come from registries—not from a filename or physical-directory count.

Open discovery catalog →

CURRENTstatus
Platform evidence status

One public answer for production identity, evidence freeze, P59, publication packages and the 0/21 DMD outcome boundary.

Object
STATE:PLATFORM:CURRENT
Claim ceiling
Status and governance only; this object does not create a biological result.
Open object →Machine record →
CURRENTclaim registry
Claim registry and evidence graph

Six versioned statements, boundaries and status records linked to their supporting evidence, limiting evidence and downstream consumers.

Object
REGISTRY:CLAIMS:CURRENT
Claim ceiling
Registering six existing statements does not create a new scientific claim; new scientific claim count remains zero.
Open object →Machine record →Evidence graph →Claim diff →
CURRENT PRODUCTION CONTENTresearch answer
Virtual Cell Query Composer 2.0

A source-constrained Research Answer Object that binds one structured DMD/ZNF133 question to eligibility, evidence, domain and OOD state, uncertainty, missing truth, next experiment and claim ceiling.

Object
REGISTRY:RESEARCH_ANSWERS:CURRENT
Claim ceiling
One registered bounded answer and zero new scientific claims; unregistered query combinations abstain without inheriting nearby evidence.
Open object →Machine record →Answer schema →Governing claims →
CURRENT PRODUCTION CONTENTexperiment plan
Experiment OS readiness plan

A machine-checkable projection of the canonical Research Answer and ZNF133 Study Card that separates ready, partial and open execution gates without authorizing an experiment.

Object
REGISTRY:EXPERIMENT_PLANS:CURRENT
Claim ceiling
Design-readiness projection only; execution and registration remain unauthorized while numeric and authority gates are open.
Open object →Machine record →Experiment Plan schema →Outcome Ledger →
CURRENT PRODUCTION CONTENToutcome ledger
Outcome Ledger

An append-only projection of registered studies, prospective predictions and measured outcomes with explicit zero semantics and governed result states.

Object
REGISTRY:OUTCOME_LEDGER:CURRENT
Claim ceiling
Zero measured outcomes means no governed experiment has returned; it is neither efficacy nor inefficacy evidence.
Open object →Machine record →Outcome Ledger schema →Experiment OS →
CURRENT PRODUCTION CONTENTinformation architecture
Research OS navigation and Trust contract

Seven canonical product destinations plus a five-domain Trust Center and an explicit compatibility ledger for stable legacy routes.

Object
CONTRACT:NAVIGATION:CURRENT
Claim ceiling
Navigation and governance discovery only; this contract creates no scientific claim, model result, experiment authorization or measured outcome.
Open object →Machine record →Evidence status →Claim registry →
CURRENT PRODUCTION CONTENTmodel evaluation contract
Model Evaluation Gateway

One rejection-first contract joining five model adapters, model-run admission, seven metric families and the G0–G7 sparse generalization cube.

Object
CONTRACT:MODEL_EVALUATION:CURRENT
Claim ceiling
Admission and evaluation governance only; zero new runs, zero DMD-calibrated models and zero new scientific claims.
Open object →Machine record →Model Center →Benchmark Suite →
CURRENT PRODUCTION CONTENTdigital tissue contract
Digital Tissue hypothesis workspace

A multiscale evidence map that joins released cell context, physical-time and spatial references to explicit perturbation, cross-cell and patient-calibration gaps.

Object
CONTRACT:DIGITAL_TISSUE:CURRENT
Claim ceiling
Hypothesis and experiment-design layer only; no cell-cell simulation, tissue rescue, patient forecast or new scientific claim.
Open object →Machine record →Cell contexts →Spatial tasks →Experiment OS →
CURRENTrelease
Current platform release manifest

The authoritative resource, schema, evidence-freeze and hosted-object boundary for the live workbench release.

Object
RELEASE:PLATFORM:CURRENT
Claim ceiling
Release identity does not expand scientific claims.
Open object →
CURRENTdirect measurement
Measured DMD context

Correction and external pathway evidence with biological-repeat-aware analyses and an explicit candidate-validation limitation.

Object
EVIDENCE:DMD:MEASURED_CONTEXT
Claim ceiling
Measured disease context; not a measured perturbation outcome for the governed 21 candidates.
Open object →Machine record →
CURRENTcomputational bridge
Candidate decision state

Current action states, blocking gaps and minimum next experiments for the 21 governed hypotheses; no therapeutic rank is generated.

Object
EVIDENCE:CANDIDATE_STATE:CURRENT
Claim ceiling
Hypothesis and next-action support only; directly measured DMD candidate outcomes remain 0/21.
Open object →Machine record →
CURRENTprospective contract
Study and outcome contracts

Draft Study Cards plus prediction and outcome schemas for prospective registration without fabricating a registered study.

Object
CONTRACT:PROSPECTIVE_STUDY:CURRENT
Claim ceiling
Design scaffold only; registered studies, predictions and outcomes remain zero until external events occur.
Open object →Machine record →
CURRENTreproducibility
Portable research snapshot

Checksummed current APIs, tables, code and provenance assembled as a portable RO-Crate source artifact.

Object
REPRO:PORTABLE_RO_CRATE:CURRENT
Claim ceiling
Reproducibility package; not a DOI deposit or independent scientific validation.
Open object →
CURRENT HOLDpublication
Falsification-first evaluation separates failure ranking from utility in perturbation transfer

Current Science Advances manuscript identity. Public scope is status only because the chemical replay produced no target score.

Object
PACKAGE:SCIENCE_ADVANCES:P59
Package state
HOLD PRIMARY SCORER FAILURE
Claim ceiling
The chemical replay produced no target score. The retained scorer failure is an engineering outcome, not evidence for or against perturbation-transfer performance or DMD efficacy.
Open object →Machine record →
CURRENT WORKINGpublication
NMD-VCell NAR curated v08 story-optimized working package

Current public NAR working package with six main figures, 31 supplementary figures and 47 governed members.

Object
PACKAGE:NAR:CURATED_V08_STORY
Package state
WORKING AUTHOR REVIEW REQUIRED NOT SUBMISSION READY
Claim ceiling
Working author-review package; technical completeness does not confer formal submission readiness.
Open object →Machine record →
FROZENpublication
Immutable v1.0.0 database-paper snapshot

Immutable database-paper publication base retained for citation and byte-level provenance.

Object
PACKAGE:DATABASE:V1.0.0
Package state
FROZEN HISTORICAL PUBLICATION BASE
Claim ceiling
This historical package does not define current scientific state.
Open object →Machine record →
SUPERSEDEDpublication
Science Advances v09.80 review packet

Earlier Science Advances review packet retained as history and explicitly superseded by P59.

Object
PACKAGE:SCIENCE_ADVANCES:V09.80
Package state
HISTORICAL SUPERSEDED BY P59
Claim ceiling
This historical package does not define current scientific state.
Open object →
HISTORICALaudit
Historical download ledger

The complete versioned-file and checksum ledger for auditors who need older or internal release identities.

Object
ARCHIVE:DOWNLOAD_AUDIT
Claim ceiling
Provenance and recovery only; directory presence is not current-package membership.
Open object →

Download hub

This legacy curated list mixes current release utilities with clearly labelled publication and reproducibility entry points. Use the governed navigator above whenever current-versus-historical identity matters.

Release manifest · current platform

Current platform release manifest

The authoritative map for v1.2.0-measured-dmd-evidence: Stage C1+C2, four disease modules, the current Workbench overlay, SQLite, APIs, schemas and checksums. Measured DMD context · 0/21 candidate perturbation outcomes.

Use
Current platform authority
Version
v1.2.0-measured-dmd-evidence
Size
JSON
SHA
see checksums
Open current manifest
Frozen publication base

Base publication snapshot manifest

The immutable v1.0.0-database-resource database-paper identity. This object preserves the older bytes and claim boundary; it is not the live platform manifest.

Use
Frozen citation base
Version
v1.0.0-database-resource
Size
JSON
SHA
b435f210…
Open base manifest
Portable release

Source-release RO-Crate

One checksummed ZIP is generated and retained with the fixed source release. Direct Sites hosting is excluded; public APIs, current tables, code, QC, the Workbench overlay and checksum manifests remain individually accessible.

Use
Portable research snapshot
Version
v1.2.0-measured-dmd-evidence
Size
Source artifact
SHA
see portable manifest
Verify RO-Crate manifest
SQLite

120-table relational database

120 non-empty tables are registered inside the source-release RO-Crate. Direct Sites hosting is excluded while typed JSON APIs remain public.

Use
Relational reuse
Version
v1.2.0-measured-dmd-evidence
Size
35.4 MB
SHA
874377d9…
Open database identity
Core TSV

Candidate-state tables

Current action, transition history and evidence-state policy; use these instead of historical ranks for current decisions.

Use
Current candidate state
Version
v1.2.0-measured-dmd-evidence
Size
7.5 KB
SHA
4c3f19d4…
Download TSV
Candidate decision contracts

What each candidate is actually for

All 21 governed hypotheses are linked to one research question, one decision available now, one blocking gap, one minimum next action and explicit supportive, null and inconclusive result rules. No target rank is generated.

Use
Candidate-to-decision reuse
Version
v1.2.0-measured-dmd-evidence
Size
JSON + TSV
SHA
resource manifest
Open JSON · Download TSV
Gene JSON / API

17,921 typed gene records

Checksum-addressable buckets plus schema 1.1 OpenAPI; no login or generated server-side score.

Use
Bulk gene API
Version
v1.2.0-measured-dmd-evidence
Size
bucketed JSON
SHA
per bucket
Open manifest · OpenAPI
Reproducibility

Checksums and file registry

Verify public bytes, object identities and release boundaries before reuse or deposition.

Use
Rebuild / verify
Version
v1.2.0-measured-dmd-evidence
Size
route bundle
SHA
checksums
Open reproducibility
Historical Science Advances packet · superseded by P59

v09.80 figure-and-manuscript review packet

All six main figures, caption book, LaTeX include, source-bound Figure 3 audit matrix and ARS Figure/Table Trace. Local staging only; not a production deployment or final submission freeze.

Use
Reviewer / submission-prep packet
Version
v09.80 scientific packet · v09.81 local staging
Size
13.1 MB zip
SHA
a840f05b…
Open packet manifest · Open manifest
Study Cards + schemas

21 draft Study Cards

YAML/TSV exports, prediction-card schema and outcome-board schema for prospective registration.

Use
Study design scaffold
Version
v1.2.0-measured-dmd-evidence
Size
YAML/TSV
SHA
manifested
Open registry · Example YAML
Stage B0 observed network

Human-myoblast perturbation network

31 published knockout hits connect to ten named complexes plus MYMK, exact fusion-screen effects, 17 individual-validation edges and two qualitative grouped CROP-seq state edges.

Use
Observed functional perturbation reuse
Version
v1.2.0-measured-dmd-evidence
Size
JSON + TSV
SHA
source manifest
Open network · Edge TSV
Stage C1 analysis extension

Candidate pathway cascade release

Measured HepG2 effects for 21 candidates, 1,360 Reactome pathway nodes, topology controls, cross-context DMD projections and explicit abstention states.

Use
Pathway cascade reuse and prospective study design
Version
PCN-v0.1-20260802
Size
JSON + TSV.GZ + PDF
SHA
analysis manifest
Open summary · Open manifest
Candidate statistical bridge

Competitive pathways and DMD-source heterogeneity

Cell-level exploratory candidate differential expression, 28,938 cameraPR tests, 1,782 direction-robust candidate-pathway pairs, 3,210 projected reversals and a prespecified prospective validation design.

Use
Statistical audit and prospective DMD experiment prioritization
Version
PCB-v0.2-20260804
Size
API + TSV.GZ + PDF
SHA
release manifest
Open summary · Open manifest
Stage C2 measured DMD evidence

Correction and external pathway validation

Biological-repeat-aware GSE272233 Reactome tests, donor/sample pseudobulk validation, sample QC, Figure 8 source data, an explicit candidate-validation limitation and a 16-check clean-room receipt.

Use
Measured disease-context analysis and reuse
Version
v1.2.0-measured-dmd-evidence
Size
API + TSV.GZ + PDF
SHA
release manifest
Open evidence · Open manifest
Platform contracts

Data, model, distribution and benchmark registries

Dataset Catalog, standardized Model Cards, the G0–G7 Benchmark Suite, a distribution-prediction schema, metric governance and challenge watch are available as typed JSON.

Use
AI-system audit and reuse
Version
v1.2.0-measured-dmd-evidence
Size
JSON + TSV
SHA
resource manifest
Data · Models · Distribution · Benchmarks
Module semantics

Eight-module meaning contract

Question, disease scope, evidence unit, output, claim ceiling and next legal handoff for every primary module, plus the disease × module capability matrix.

Use
Interpretation and navigation audit
Version
v1.2.0-measured-dmd-evidence
Size
JSON + TSV
SHA
resource manifest
Open meaning map · JSON · TSV

Current identity

Three objects define the current release candidate

Analysis core

FILE:CORE:v0.8.1:v24r1:20260722

nmd_vcell_database_resource_v0.8.1-v24r1-20260722.tar.gz

9,677,910 bytes · SHA b88a3b9f1ae4…

SQLite

FILE:SQLITE:v0.9.2:schema1.1:20260725

nmd_vcell_sqlite_v0.9.2_schema1.1_20260725.sqlite

37,122,048 bytes · SHA 874377d932b6…

Workbench overlay

FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.106:20260904

nmd_vcell_research_workbench_overlay_v1.2.0_measured_dmd_evidence_20260904_stage5_106.tar.gz

Read identity object

Current public workbench releasev1.2.0-measured-dmd-evidenceComposite identity · b435f2100bad…
Analysis corev0.8.1FILE:CORE:v0.8.1:v24r1:20260722
Relational payloadSQLite schema 1.1FILE:SQLITE:v0.9.2:schema1.1:20260725
Workbench overlayv1.0FILE:OVERLAY:v1.2.0-measured-dmd-evidence:stage5.106:20260904
Browse all audit files
Two identities, one explicit relationship: use the current platform manifest for the live workbench and the base publication snapshot manifest for the frozen citation base. Formal DOI deposition, institution-approved licences and final maintainer metadata remain external release gates.