P001 · Completed research project

Molecular State Explorer

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.

COMPLETED RESEARCH

Model artifact: candidate — not released for inference. Research use only; not for clinical decision-making.

Open research scorer

Research status: Completed
Model artifact: Candidate
Evidence record: Frozen
Immutable releases: 0

P001 · Completed study

Completed research with a reviewable candidate model.

The scientific project is complete. The model artifact remains a research candidate while its frozen evidence and provenance remain available for independent review.

Overview

T001 · Scientific question

Research-only estimation of the TP53 somatic-mutation-state label from TCGA-BRCA bulk RNA expression.

Indication: TCGA-BRCA
Input: bulk RNA expression (GDC STAR-Counts tpm_unstranded as log2(TPM + 1))
Target: TP53 somatic-mutation-state label

Workflow

Declared research workflow

TCGA-BRCA
RNA expression
P001 preprocessing
TP53 somatic-mutation-state label model
candidate research result

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.

Model artifact

Candidate model

tcga-brca-tp53-logreg-1.0.0

Checksum: sha256:0d5a50eb0b881d749e6eb43535eb8583d63fdae866ae7abc421b9aa0543a0707

The research project is complete; this model artifact has not been released for public inference or clinical use.

Reproducibility

Reference parity verified

Absolute difference: 5.551115123125783e-17 (tolerance 1e-12).

Review package: available; frozen for independent review; no approval recorded

Provenance

Public-safe source summary

NCI Genomic Data Commons open processed data

Data Release 45.0 - December 04, 2025 · compatibility source: AmbioSpire single-project platform

Limitations

Research-use 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 and educational use only; not diagnosis, medical advice, or clinical decision support.

Study contract

Reproducible inputs and outputs.

These contracts describe the completed study interface and remain separate from the candidate model's release status.

Inputs

Required artifacts

No upstream artifact types declared.

Outputs

Produced artifacts

FeatureEvidence@2.0.0
MolecularSignature@2.0.0
MolecularStatePrediction@1.0.0

Registry

Dataset requests

GDC_TCGA_BRCA_CASE_METADATA @ pending-source-lock
GDC_TCGA_BRCA_RNA @ pending-source-lock
GDC_TCGA_BRCA_SOMATIC_MUTATIONS @ pending-source-lock

Dependency position

Typed evidence in. Versioned evidence out.

Upstream

No upstream project dependencies.

Downstream

P002 · Cancer Vulnerability ExplorerConsumes this project as an upstream release

FeatureEvidence@2.0.0, MolecularSignature@2.0.0

Immutable records

Releases and artifact envelopes.

Scaffold declarations and completed release records are intentionally separate.

Registry ready

Model artifact not released

The research project is complete. No immutable model release has been issued; the validated candidate remains research-only.

Review the release contract

Web manifest

Declared project routes.

Route metadata is registered with the project instead of being enumerated in platform navigation code.

Overview

Research-only scaffold

Registration is not evidence of analytical completion, scientific validity, medical utility, or clinical readiness.