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Model v22.86 Evidence Cycles.External Cohort set34.Jun 2026
Research Intelligence

Knowledge Graph, Contracts & Toolchains

Interactive 3D knowledge graph over research entities, API contract explorer for Pass 42, Toolchain Workbench for Pass 43, and Pass99 model-readiness evidence for governed research triage.

Model Readiness Endpoint

The readiness route exposes final sign-off, endpoint status, manifest replay, and use boundaries before any v24 research score is consumed.

Endpoint readinessready for research triage endpoint
Use boundaryprohibited
Scoring interface.venv-training/bin/python scripts/python/score_v24_research_genes_v1.py --threshold 0.71 GENE_SYMBOL
Model IDv24_source_feature_integration
Final Sign-offapproved for research triage use
Candidate Threshold0.71
Manifest Replaypassed
Set41 Surveillanceset41 surveillance passed
Readiness JSON/api/research/model-readiness
Readiness JSONv24_endpoint_readiness_contract_v1.jsonv24_final_governance_signoff_v1.json

3D Knowledge Graph

Filter by node group and text to isolate specific evidence pathways.

Pass42 Command Center

Interactive control room for API contracts and Dockerized molecular/3D runtime probes.

3D-Beacons OpenAPI2.7.1

paths 9 · ops 9

VolumeServer OpenAPI0.9.7

paths 3

OpenMM Latest Release8.5.1

2026-04-10T19:10:21Z

PTEN Structures (3D-Beacons)22

provider-mixed evidence channel

MethodPathSummaryTags
GET/annotations/{uniprot_qualifier}.jsonGet annotations for a UniProt residue rangeAnnotations
GET/ensembl/summary/{qualifier}.jsonGet Ensembl SummaryEnsembl
GET/health/Health Checkn/a
GET/sequence/resultResultSequence
POST/sequence/searchSearchSequence
GET/sequence/summarySequence SummarySequence
POST/uniprot/summaryGet List Of Uniprot SummaryUniProt
GET/uniprot/summary/{qualifier}.jsonGet Uniprot SummaryUniProt
GET/uniprot/{qualifier}.jsonGet UniprotUniProt

Tag Operation Mix

UniProt3
Sequence3
Ensembl1
Annotations1

PTEN Provider Mix

PDBe16
AlphaFold DB3
SWISS-MODEL1
AlphaFill1
isoform.io1

VolumeServer Sample Payloads

xray_1cbs_cell_d0205.4 KB
em_emd_30210_cell_d0114.8 KB

OpenUSD Deployment Signals

OpenUSD49
Docker9
usd-exchange9
container9
Python wheels7
manylinux1
OpenMM release pagepass42_source_contracts_summary.jsonpass42_source_contracts_raw.json

Pass43 Toolchain Workbench

New source intelligence and live Docker execution layer for 3D/molecular tooling.

Short Sequence Submit202
PTEN Sequence Submit202
PDBFixer README Lines27

Blender CLI

--python6
--background5
--render-frame5
--render-output4
--cycles-device2
--help2
--python-expr1

MDAnalysis

AtomGroup213
moment_of_inertia6
radius_of_gyration3
center_of_mass3
RMSD0

MDTraj

compute_rg6
mass5
trajectory2
radius of gyration2

Biotite

sasa16
AtomArray3
probe_radius2
vdw_radii2
surface area1

PDBFixer

PDBFixer8
openmm3
findMissingResidues0
findMissingAtoms0
addMissingAtoms0
addMissingHydrogens0

MolViewSpec

volume20
download6
parse6
Volume Server5
ebi.ac.uk/pdbe/densities2
maps.rcsb.org1
3D-Beacons sequence poll status 20210
pass43_source_tooling_summary.jsonpass43_docker_runtime_summary.json

Artifact Launchpad

Direct links into repository-backed files served via Next.js route handlers. 67 artifacts indexed.

Model Readiness Endpoint/api/research/model-readinessClinical Readiness Endpoint/api/research/clinical-readinessPatient Validation Endpoint/api/research/patient-validationRetrospective Validation Endpoint/api/research/retrospective-validationExternal Validation Intake Endpoint/api/research/external-validation-intakeRetrospective Acceptance Endpoint/api/research/retrospective-acceptanceCohort Admissibility Endpoint/api/research/cohort-admissibilitySource Manifest Endpoint/api/research/source-manifestSource Manifest Completion Endpoint/api/research/source-manifest-completionCohort Intake Preflight Endpoint/api/research/cohort-intake-preflightFrozen Scoring Handoff Endpoint/api/research/frozen-scoring-handoffRetrospective Validation Launch Endpoint/api/research/retrospective-validation-launchProspective Validation Readiness Endpoint/api/research/prospective-validation-readinessRetrospective Cohort Evidence Endpoint/api/research/retrospective-cohort-evidenceRetrospective Execution Bundle Endpoint/api/research/retrospective-execution-bundleReal Cohort Intake Packet Endpoint/api/research/real-cohort-intake-packetPass112 Dossier Bridge Endpoint/api/research/pass112-dossier-bridgePass100 Clinical Translation Readinessartifacts/downloads/training/pass100_clinical_translation_readiness_v1.jsonPass101 Patient-Level Validationartifacts/downloads/training/pass101_patient_level_validation_protocol_v1.jsonPass101 Cohort Templateartifacts/downloads/training/pass101_patient_level_validation_cohort_template_v1.csvPass102 Retrospective Validationartifacts/downloads/training/pass102_retrospective_validation_dry_run_v1.jsonPass102 Score Templateartifacts/downloads/training/pass102_patient_validation_score_template_v1.csvPass103 External Validation Intakeartifacts/downloads/training/pass103_external_validation_intake_package_v1.jsonPass103 Candidate Score Inputartifacts/downloads/training/pass103_external_validation_candidate_score_input_v1.csvPass104 Retrospective Acceptanceartifacts/downloads/training/pass104_retrospective_acceptance_gate_dry_run_v1.jsonPass104 Acceptance Policyartifacts/downloads/training/pass104_retrospective_acceptance_gate_policy_v1.jsonPass105 Cohort Admissibilityartifacts/downloads/training/pass105_cohort_admissibility_dry_run_v1.jsonPass106 Source Manifestartifacts/downloads/training/pass106_source_manifest_template_v1.jsonPass107 Source Manifest Completionartifacts/downloads/training/pass107_source_manifest_completion_packet_v1.jsonPass108 Cohort Intake Preflightartifacts/downloads/training/pass108_cohort_intake_preflight_dry_run_v1.jsonPass109 Frozen v24 Scoring Handoffartifacts/downloads/training/pass109_frozen_v24_scoring_handoff_v1.jsonPass109 Frozen Score Schemaartifacts/downloads/training/pass109_frozen_v24_score_schema_v1.jsonPass110 Retrospective Validation Launchartifacts/downloads/training/pass110_retrospective_validation_launch_dry_run_v1.jsonPass110 Launch Suite Summaryartifacts/downloads/training/pass110_retrospective_validation_launch_suite_summary_v1.jsonPass111 Prospective Validation Readinessartifacts/downloads/training/pass111_prospective_validation_readiness_v1.jsonPass111 Prospective Protocolartifacts/downloads/training/pass111_prospective_validation_protocol_v1.jsonPass111 Event Schemaartifacts/downloads/training/pass111_prospective_event_schema_v1.jsonPass111 Event Templateartifacts/downloads/training/pass111_prospective_event_template_v1.csvPass112 Retrospective Cohort Evidenceartifacts/downloads/training/pass112_retrospective_cohort_evidence_dossier_v1.jsonPass112 Evidence Schemaartifacts/downloads/training/pass112_retrospective_cohort_evidence_schema_v1.jsonPass112 Evidence Templateartifacts/downloads/training/pass112_retrospective_cohort_evidence_template_v1.jsonPass113 Retrospective Execution Bundleartifacts/downloads/training/pass113_retrospective_execution_bundle_v1.jsonPass113 Execution Runbookartifacts/downloads/training/pass113_retrospective_execution_runbook_v1.jsonPass114 Real Cohort Intake Packetartifacts/downloads/training/pass114_real_cohort_intake_packet_v1.jsonPass114 Owner Upload Manifestartifacts/downloads/training/pass114_real_cohort_upload_manifest_template_v1.jsonPass114 Owner Checklistartifacts/downloads/training/pass114_real_cohort_owner_checklist_v1.jsonPass115 Pass112 Dossier Bridgeartifacts/downloads/training/pass115_pass112_dossier_bridge_v1.jsonPass115 Generated Pass112 Dossierartifacts/downloads/training/pass115_generated_pass112_dossier_v1.jsonPass115 Dossier Field Mappingartifacts/downloads/training/pass115_pass112_dossier_field_mapping_v1.jsonPass99 Final Governance Sign-offartifacts/downloads/training/v24_final_governance_signoff_v1.jsonv24 Endpoint Readiness Contractartifacts/downloads/training/v24_endpoint_readiness_contract_v1.jsonPass99 Manifest Replayartifacts/downloads/training/v24_manifest_replay_pass99_v1.jsonCombined Findings Brief/passesLatest Research Reportresearch-passes/pass-115-pass112-dossier-bridge.htmlCombined Findings JSONartifacts/downloads/research-summary/latest_combined_findings_v1.jsonset41 Suite Summaryartifacts/downloads/training/set41_suite_summary_v1.jsonTraining Readiness Overviewbiomarker-training-readiness-overview.htmlTraining Readiness Markdownbiomarker-training-readiness-overview.mdResearch Metrics v2artifacts/downloads/research_metrics_v2.jsonLatest v24 Training Reportartifacts/downloads/training/ndd_model_training_report_v24_source_feature_integration.jsonPrevious v23 Training Reportartifacts/downloads/training/ndd_model_training_report_v23_set35_comparator_repair.jsonv24 Source Feature Tableartifacts/downloads/source-integration/v24_source_feature_table_v1.jsonv11 vs v10 Significanceartifacts/downloads/training/set11_v11cal_vs_v10_significance_v1.jsonset41 v24_sf vs v10 Significanceartifacts/downloads/training/set41_v11cal_vs_v10_significance_v1.jsonv11 vs v4 Significanceartifacts/downloads/training/set11_v11cal_vs_v4_significance_v1.jsonSet11 Policy Evalartifacts/downloads/training/set11_policy_eval_v1.jsonset41 Policy Evalartifacts/downloads/training/set41_policy_eval_v1.json