module_id	label	route	status	disease_scope	research_question	evidence_unit	current_output	claim_ceiling	next_handoff	next_route
diseases	Diseases	/resource/diseases/	FOUR_DISEASE_TYPED_EVIDENCE_AVAILABLE	DMD, FSHD, DM1 and SMA disease-specific evidence modules; each retains its own biological model, statistical unit and claim ceiling.	What has been measured, induced, corrected, perturbed or remains missing in each disease?	Dataset-specific biological unit—donor, biopsy, clone, well or donor-derived line; individual cells are not treated as independent biological replicates by default.	Typed disease summary, dataset registry, role-typed candidate objects, strict evidence states and a disease-specific next experiment.	No pooled cross-disease score, disease winner, treatment ranking, calibrated patient simulation or clinical recommendation.	Choose a disease route; use the DMD interactive workflow where supported or follow the disease-specific next experiment.	/resource/diseases/compare/
questions	Questions	/resource/virtual-cell/	DMD_INTERACTIVE_GATE_OTHER_DISEASES_EVIDENCE_ONLY	The interactive six-input predictability checker is DMD-specific. FSHD, DM1 and SMA currently expose bounded evidence routes, not an inference engine.	Can the current release answer this prespecified DMD cell-state perturbation question?	One question object with disease, cell state, perturbation, time, endpoint and requested output fixed together.	Answer state, available evidence layers, missing truth, claim boundary and the next discriminating experiment.	No calibrated DMD response, candidate pathway outcome, patient trajectory, efficacy estimate or clinical recommendation.	Inspect the relevant context in Browse, then compare DMD candidate evidence or freeze a Study Card.	/resource/cell-browser/
browse	Browse	/resource/cell-browser/	DMD_CONTEXT_MAP_AND_SOURCE_LINKED_RECORDS_AVAILABLE	The interactive cell-compartment map is DMD muscle context. Four-disease datasets and measured evidence are browsed through the disease atlas.	Which gene, cell compartment, dataset and measured context are relevant to the question?	A source-linked gene, dataset or compartment record with explicit provenance and biological/statistical unit.	A context map or stable evidence record that shows what is observed, contextual and missing.	No cell-specific causal effect, cell–cell interaction estimate or perturbation-conditioned DMD fate is inferred from browsing.	Open a gene record, compare DMD candidates, or return to a disease module for disease-level evidence.	/resource/genes/
gene_compare	Gene compare	/resource/compare	DMD_EVIDENCE_DIMENSION_COMPARISON_AVAILABLE	Compares mapped gene and DMD-candidate evidence dimensions. Disease-level comparison is a separate categorical route.	How do selected genes differ across evidence depth, source agreement, context and the experiment-blocking gap?	One mapped gene record per identifier, preserving original input, mapping provenance and separate evidence dimensions.	A stable comparison object and rule-traced gap-closing study suggestion without a scalar winner.	No target rank, therapeutic priority, pooled cross-disease score or silent conversion of missing evidence to zero.	Send the selected evidence gap to Design and freeze the estimand, endpoint and stopping rule.	/resource/planner
design	Design	/resource/planner	TWENTY_ONE_DMD_DRAFT_STUDY_CARDS_AVAILABLE	Versioned Study Cards currently cover the 21 governed DMD candidates. Other disease modules provide bounded next-experiment recommendations, not registered Study Cards.	What falsifiable experiment would close the named evidence gap and what result would change the decision?	One versioned Study Card with estimand, endpoint, replication, QC, analysis and stopping rule.	A downloadable draft design object with explicit registration gaps and links to its evidence inputs.	A draft is not a registered study, executed experiment, measured outcome, target validation or efficacy result.	Inspect lifecycle state in Registry; registration and execution remain prospective.	/resource/registry
models	Models	/resource/models/	BOUNDED_MODELRUN_LEDGER_NO_CALIBRATED_DISEASE_MODEL	Frozen DMD/assay benchmark runs and model audits are available. FSHD, DM1 and SMA do not currently have calibrated NMD-VCell model runs.	What actually ran on a frozen task, against which baseline, with which split, metric, failure reason and permitted use?	One ModelRun bound to a task, data revision, split, baseline, seed, metrics and gate decision.	Model cards, a six-run execution ledger, benchmark contracts, negative results and explicit readiness gates.	Published external performance is not inherited; no calibrated DMD or multi-disease predictor is released.	Carry only a frozen, gate-passing run into prospective registration and outcome comparison.	/resource/registry
registry	Registry	/resource/registry	READ_ONLY_LIFECYCLE_AND_EVIDENCE_REGISTRY_AVAILABLE	Two layers are explicit: the DMD prospective lifecycle and the released four-disease evidence contract.	What is draft, frozen, registered, running, measured, released, superseded or intentionally absent?	One immutable versioned research object; a missing record is never interpreted as a negative result.	Lifecycle states for comparisons, Study Cards, protocols, ModelRuns, predictions and outcomes, including honest zero states.	The public registry is read-only; it does not accept uploads, create persistence or promote zero outcomes into validation.	Contribute a traceable outcome or evidence object, then apply the formal transition rules.	/resource/contribute/
data_api	Data & API	/resource/downloads	VERSIONED_MACHINE_READABLE_OBJECTS_AVAILABLE	Covers the DMD workbench and the additive four-disease v2 evidence contract through versioned files and static APIs.	Which exact bytes, schema, identifier, checksum and release boundary support a displayed result?	One versioned file or API object with a declared schema, provenance path and checksum identity.	JSON, TSV, schemas, manifests, checksums, release bundles and a portable RO-Crate contract.	Machine readability or file availability does not expand biological claims; hosting exclusions remain declared rather than silently omitted.	Verify the object, then return to the module whose scientific question it supports.	/resource/meaning-map/