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T001 includes metadata and read-only compatibility validation for the completed legacy TCGA-BRCA TP53 candidate. The current platform specification remains unapproved and cannot pass G0 or produce a release.","entrypoint":"pipeline.project:MolecularStateExplorerProject","produced_artifacts":["FeatureEvidence@2.0.0","MolecularSignature@2.0.0","MolecularStatePrediction@1.0.0"],"project_id":"P001","project_name":"Molecular State Explorer","required_artifacts":[],"schema_version":"1.0.0","slug":"molecular-state-explorer","status":"active","validation_gates":["G0","G1","G2","G3","G4","G5","G6","G7"],"version":"0.3.0","web":{"enabled":true,"navigation":{"category":"Explorers","label":"Molecular State Explorer","order":10},"routes":[{"label":"Overview","path":"/projects/molecular-state-explorer"}]},"summary":"Research-only molecular-state modeling project with independently versioned task contracts. T001 includes metadata and read-only compatibility validation for the completed legacy TCGA-BRCA TP53 candidate. The current platform specification remains unapproved and cannot pass G0 or produce a release.","research_only":true,"scaffold":false,"candidate_presentation":{"project_id":"P001","project_title":"Molecular State Explorer","task_id":"T001","scientific_question":"Research-only estimation of the TP53 somatic-mutation-state label from TCGA-BRCA bulk RNA expression.","indication":"TCGA-BRCA","input_modality":"bulk RNA expression (GDC STAR-Counts tpm_unstranded as log2(TPM + 1))","target":"TP53 somatic-mutation-state label","methodology_summary":"The declared P001/T001 preprocessing contract is applied to bulk RNA expression (GDC STAR-Counts tpm_unstranded as log2(TPM + 1)) before the checksummed candidate is assessed.","workflow":["TCGA-BRCA","RNA expression","P001 preprocessing","TP53 somatic-mutation-state label model","candidate research result"],"candidate":{"model_id":"tcga-brca-tp53-logreg-1.0.0","model_checksum":"sha256:0d5a50eb0b881d749e6eb43535eb8583d63fdae866ae7abc421b9aa0543a0707","status":"candidate","release_status":"not_released"},"reproducibility":{"state":"verified","absolute_difference":5.551115123125783e-17,"tolerance":1e-12},"provenance":{"source":"NCI Genomic Data Commons open processed data","data_release":"Data Release 45.0 - December 04, 2025","legacy_platform":"AmbioSpire single-project platform","synthetic":false,"patient_level_data_in_presentation":false},"review_package":{"availability":"available","status":"frozen for independent review; no approval recorded","package_checksum":"sha256:9cb965c32eb7e99da60847895bfb905edcde573d6881a1a88a6a247a161a1991","reviewed_git_commit":"fc75d67dba38c3c0ae41847036bca422b79960d2","independent_approval_recorded":false},"limitations":["Retrospective single-cohort internal evaluation only; no external validation.","Bulk tumor expression is affected by subtype, purity, batch, and technical factors.","Feature coefficients are associations and must not be interpreted causally.","Expression-based estimation is not a substitute for mutation testing.","The compact candidate payload and patient-level working data are not included in this package."],"research_use_only":true,"clinical_use":false}},{"datasets":[{"dataset_id":"DEPMAP_CRISPR_GENE_EFFECT","layer":"CURATED","required":true,"version":"pending-source-lock"},{"dataset_id":"GDC_TCGA_BRCA_RNA","layer":"CURATED","required":true,"version":"pending-source-lock"},{"dataset_id":"GDSC_DRUG_RESPONSE","layer":"CURATED","required":true,"version":"pending-source-lock"},{"dataset_id":"PDC_PROTEOMICS","layer":"CURATED","required":true,"version":"pending-source-lock"},{"dataset_id":"PRISM_DRUG_RESPONSE","layer":"CURATED","required":true,"version":"pending-source-lock"}],"dependencies":[{"minimum_release":"1.0.0","project_id":"P001","required_artifacts":["FeatureEvidence@2.0.0","MolecularSignature@2.0.0"]}],"description":"Contract scaffold for integrating molecular-state evidence with functional, pharmacological, and proteomic evidence to evaluate candidate vulnerabilities. No vulnerability analysis or validation is implemented.","entrypoint":"pipeline.project:CancerVulnerabilityExplorerProject","produced_artifacts":["CandidateVulnerability","DrugResponseEvidence","FunctionalDependency","ProteinValidationEvidence"],"project_id":"P002","project_name":"Cancer Vulnerability Explorer","required_artifacts":["FeatureEvidence@2.0.0","MolecularSignature@2.0.0"],"schema_version":"1.0.0","slug":"cancer-vulnerability-explorer","status":"scaffold","validation_gates":["G0","G1","G2","G3","G4","G5","G6","G7"],"version":"0.1.0","web":{"enabled":true,"navigation":{"category":"Explorers","label":"Cancer Vulnerability Explorer","order":20},"routes":[{"label":"Overview","path":"/projects/cancer-vulnerability-explorer"}]},"summary":"Contract scaffold for integrating molecular-state evidence with functional, pharmacological, and proteomic evidence to evaluate candidate vulnerabilities. No vulnerability analysis or validation is implemented.","research_only":true,"scaffold":true,"candidate_projections":[]},{"datasets":[],"dependencies":[],"description":"Research-only contract scaffold for a tumor-normal whole-genome somatic SNV/indel caller generalization benchmark. No scientific execution, validation, or release is implemented.","entrypoint":"pipeline.project:CancerGenomeVariantExplorerProject","produced_artifacts":[],"project_id":"P003","project_name":"Cancer Genome Variant Explorer","required_artifacts":[],"schema_version":"1.0.0","slug":"cancer-genome-variant-explorer","status":"scaffold","task_registry":"tasks/registry.yaml","validation_gates":["G0","G1","G2","G3","G4","G5","G6","G7"],"version":"0.1.0","web":{"enabled":false,"navigation":{"category":"Explorers","label":"Cancer Genome Variant Explorer","order":30},"routes":[]},"summary":"Research-only contract scaffold for a tumor-normal whole-genome somatic SNV/indel caller generalization benchmark. No scientific execution, validation, or release is implemented.","research_only":true,"scaffold":true,"candidate_projections":[]}]}