{ "registry_schema": "nmd-vcell-tool-catalog-registry/1.0", "interface_build": "EA-20260817-57", "resource_release": "v1.2.0-measured-dmd-evidence", "checked_at": "2026-08-16", "route": "/resource/tools/", "tool_count": 7, "records": [ { "tool_id": "TOOL-GENE-RESOLVER-1.0", "title": "Gene Resolver", "category": "IDENTITY", "audience": [ "biologist", "data steward", "model developer" ], "execution_state": "LIVE_WEB_WORKFLOW", "primary_question": "Which canonical gene does this symbol, alias, previous symbol or identifier resolve to?", "input_contract": { "required": [ "gene symbol, alias, Ensembl ID or NCBI Gene ID" ], "example": "P53 or ENSG00000141510" }, "output_contract": { "object": "Gene search result", "includes": [ "canonical symbol", "stable gene route", "mapping state", "released evidence pointers" ] }, "prerequisites": [ "Use one identifier per lookup", "Treat ambiguous aliases as unresolved until manually checked" ], "suitability_rule": "Suitable for identifier normalization and navigation; not a biological inference engine.", "failure_states": [ { "code": "IDENTIFIER_NOT_FOUND", "meaning": "No released mapping key matches the input.", "next_action": "Check source species, namespace and spelling." }, { "code": "AMBIGUOUS_ALIAS", "meaning": "The alias cannot be assigned safely to one canonical symbol.", "next_action": "Use Ensembl or NCBI Gene ID." } ], "responsible_use": [ "Do not interpret successful identity resolution as evidence of disease relevance." ], "web_route": "/resource/search", "api_routes": [ "/resource/api/v1.1/identifier_mapping.json", "/resource/api/v1/search_index.json" ], "next_handoff": { "label": "Open the canonical Gene object", "route": "/resource/genes/" }, "inspired_by": [ "Cellarium task-specific tool identity", "CZI linked object navigation" ] }, { "tool_id": "TOOL-EVIDENCE-COMPARATOR-1.0", "title": "Evidence Comparator", "category": "EVIDENCE", "audience": [ "biologist", "translational researcher" ], "execution_state": "LIVE_WEB_WORKFLOW", "primary_question": "How do several genes differ across evidence dimensions without forcing a winner?", "input_contract": { "required": [ "two or more gene identifiers" ], "example": "ZNF133, GFOD2, SEMA3C" }, "output_contract": { "object": "Frozen Comparison", "includes": [ "dimension matrix", "missingness", "source links", "claim boundary" ] }, "prerequisites": [ "Resolve every input to a canonical gene", "Interpret not assessed separately from negative evidence" ], "suitability_rule": "Suitable for side-by-side evidence inspection; not suitable for therapeutic ranking.", "failure_states": [ { "code": "GENE_NOT_ASSESSED", "meaning": "A dimension has no released evidence for one or more genes.", "next_action": "Open the gene page and inspect the missing-edge experiment." }, { "code": "COMPARISON_NOT_FROZEN", "meaning": "The requested set has no immutable comparison object.", "next_action": "Create a shareable comparison from the compare route." } ], "responsible_use": [ "Do not convert a comparison into a clinical or therapeutic recommendation." ], "web_route": "/resource/compare", "api_routes": [ "/resource/api/v1.3/research-objects/registry.json" ], "next_handoff": { "label": "Turn a gap into a Study Card", "route": "/resource/planner" }, "inspired_by": [ "CZI associated resources", "Cellarium biological-question framing" ] }, { "tool_id": "TOOL-PROCESS-INSPECTOR-1.0", "title": "Process Inspector", "category": "MECHANISM", "audience": [ "biologist", "experimental scientist" ], "execution_state": "LIVE_READ_ONLY", "primary_question": "Which observed, contextual or hypothesized edges connect a candidate to a DMD process?", "input_contract": { "required": [ "process node, edge or candidate" ], "example": "regeneration or ZNF133" }, "output_contract": { "object": "Process-map view", "includes": [ "node state", "edge evidence class", "claim ceiling", "missing-edge experiment" ] }, "prerequisites": [ "Keep observed reference edges separate from DMD hypotheses" ], "suitability_rule": "Suitable for mechanism navigation and experiment design; not a causal simulator.", "failure_states": [ { "code": "EDGE_NOT_VALIDATED_IN_DMD", "meaning": "The edge is contextual or hypothesized rather than a validated DMD transition.", "next_action": "Use the named missing-edge experiment." } ], "responsible_use": [ "Do not describe a pathway edge as a predicted cell-state transition unless a registered model and matched truth support it." ], "web_route": "/resource/process/", "api_routes": [ "/resource/api/v1.1/perturbation_cascade_network.json", "/resource/api/v1.1/human_myoblast_perturbation_network.json" ], "next_handoff": { "label": "Design the missing-edge study", "route": "/resource/planner" }, "inspired_by": [ "Recursion physical–digital loop", "Cellarium applicability notes" ] }, { "tool_id": "TOOL-MODEL-AUDITOR-1.0", "title": "Model Auditor", "category": "MODEL", "audience": [ "model developer", "reviewer" ], "execution_state": "LIVE_READ_ONLY", "primary_question": "What exact task ran, against which baselines, and why did the gate pass, fail or stop?", "input_contract": { "required": [ "registered ModelRun" ], "example": "MRUN-GEARS-0.1.2-FIVE-SEED-20260713" }, "output_contract": { "object": "ModelRun Release", "includes": [ "frozen task", "metrics", "baseline decision", "reproduction receipt", "prohibited uses" ] }, "prerequisites": [ "A run must exist in the immutable ModelRun ledger" ], "suitability_rule": "Suitable for audit and model selection within the frozen task; external reputation is not accepted as local performance.", "failure_states": [ { "code": "PARTIAL_REPRODUCTION_RECEIPT", "meaning": "Code, container, data digest or seed receipt is missing.", "next_action": "Do not claim clean-room reproducibility; inspect the explicit missing fields." }, { "code": "TASK_CONTEXT_MISMATCH", "meaning": "The run context does not qualify the requested disease prediction.", "next_action": "Return to the Dataset Card and task contract." } ], "responsible_use": [ "Completed does not mean calibrated for DMD, therapeutic use or clinical use." ], "web_route": "/resource/models/", "api_routes": [ "/resource/api/v1.1/model_run_registry.json", "/resource/api/v1.1/model_run.schema.json" ], "next_handoff": { "label": "Inspect benchmark gates", "route": "/resource/benchmarks" }, "inspired_by": [ "CZI model detail and quickstart pattern", "Tahoe versioned release object" ] }, { "tool_id": "TOOL-METHOD-NAVIGATOR-1.0", "title": "Method Navigator", "category": "METHOD", "audience": [ "biologist", "model developer", "reviewer" ], "execution_state": "LIVE_READ_ONLY", "primary_question": "Which model family, permanent baselines and evaluation layers fit this frozen biological task?", "input_contract": { "required": [ "task contract", "available data context", "desired output object" ], "example": "unseen perturbation × DMD myogenic cells × population distribution" }, "output_contract": { "object": "Method compatibility view", "includes": [ "candidate model families", "minimum data contract", "permanent baselines", "evaluation requirements", "next gate" ] }, "prerequisites": [ "Freeze the biological unit and holdout axis", "Declare whether the output is a mean vector, cell distribution or functional endpoint" ], "suitability_rule": "Suitable for method selection and review; it does not execute a model or transfer literature performance into NMD-VCell.", "failure_states": [ { "code": "TASK_NOT_FROZEN", "meaning": "The biological unit, output or generalization axis is undefined.", "next_action": "Write the task and split contract before choosing an architecture." }, { "code": "TRUTH_CONTEXT_MISSING", "meaning": "No matched outcome exists for the requested disease and cell state.", "next_action": "Return an abstention and open the Experiment Planner." }, { "code": "BASELINE_NOT_REGISTERED", "meaning": "The advanced model has no task-compatible simple comparator.", "next_action": "Register zero-change, mean, linear or nearest-neighbor controls first." } ], "responsible_use": [ "Source-reported capability is a method reference, not a local benchmark result or DMD validation." ], "web_route": "/resource/technology-methods/", "api_routes": [ "/resource/api/v1.1/technical_method_registry.json" ], "next_handoff": { "label": "Audit an executed ModelRun", "route": "/resource/models/" }, "inspired_by": [ "CZI standardized benchmark tasks", "Systema perturbation-specific evaluation", "AnnData typed data contracts" ] }, { "tool_id": "TOOL-EXPERIMENT-PLANNER-1.0", "title": "Experiment Planner", "category": "EXPERIMENT", "audience": [ "experimental scientist", "translational researcher" ], "execution_state": "LIVE_DRAFT_BUILDER", "primary_question": "What prospective study would resolve the current decision-blocking evidence gap?", "input_contract": { "required": [ "canonical candidate", "biological context", "endpoint and comparator intent" ], "example": "ZNF133 × DMD myogenic state × fusion endpoint" }, "output_contract": { "object": "Draft Study Card", "includes": [ "estimand", "controls", "endpoint", "decision rule", "return path" ] }, "prerequisites": [ "Candidate identity resolved", "Current evidence gap inspected", "Draft must be reviewed before registration" ], "suitability_rule": "Suitable for drafting a falsifiable study; the output is not a registered protocol or prediction.", "failure_states": [ { "code": "UNKNOWN_GENE", "meaning": "The candidate cannot be resolved to the released identifier map.", "next_action": "Use Gene Resolver first." }, { "code": "INCOMPLETE_STUDY_CONTRACT", "meaning": "Context, comparator, endpoint or decision rule is missing.", "next_action": "Complete all required Study Card fields before review." } ], "responsible_use": [ "A draft Study Card must not be represented as an approved or executed experiment." ], "web_route": "/resource/planner", "api_routes": [ "/resource/api/v1.1/registered_studies.json" ], "next_handoff": { "label": "Review registry lifecycle", "route": "/resource/registry" }, "inspired_by": [ "Recursion experiment loop", "CZI responsible-use and prerequisite sections" ] }, { "tool_id": "TOOL-OUTCOME-REGISTRY-1.0", "title": "Outcome Registry Inspector", "category": "OUTCOME", "audience": [ "reviewer", "data steward", "experimental scientist" ], "execution_state": "LIVE_READ_ONLY_EMPTY_REGISTRY", "primary_question": "Has a draft study become registered, predicted, measured and returned to the evidence graph?", "input_contract": { "required": [ "study, prediction or outcome identifier" ], "example": "future registered study ID" }, "output_contract": { "object": "Lifecycle receipt", "includes": [ "state", "immutability", "linked prediction", "measured outcome", "evidence return" ] }, "prerequisites": [ "A prospective study must pass review and registration before an outcome can be attached" ], "suitability_rule": "Suitable for lifecycle audit. The currently empty registries are a truthful state, not missing UI content.", "failure_states": [ { "code": "NO_REGISTERED_OBJECT", "meaning": "No immutable study, prediction or outcome exists for the identifier.", "next_action": "Return to the draft planner and registration gate." }, { "code": "OUTCOME_NOT_RETURNED", "meaning": "A registered study lacks a measured outcome or evidence-graph return.", "next_action": "Complete the governed outcome import." } ], "responsible_use": [ "Do not fabricate outcome rows or infer efficacy from an empty registry." ], "web_route": "/resource/registry", "api_routes": [ "/resource/api/v1.1/registered_studies.json", "/resource/api/v1.1/experimental_outcomes.json" ], "next_handoff": { "label": "Return to Evidence Atlas", "route": "/resource/diseases/" }, "inspired_by": [ "Recursion closed loop", "CZI associated resources and prohibited-use sections" ] } ], "boundary": "A tool route exposes a governed workflow and its failure states. It does not imply that every requested computation, prediction or outcome is available." }