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Flagship Run Registry

This page names the runtime-owned flagship public runs that are actually checked in today. It is the runtime answer to a simple question:

Which public benchmark runs can I open right now, and what do they really authorize?

Reading Rule

  • treat the registry as the shortest answer to what the runtime package is actually willing to stand behind today
  • read run bundles, stage lineage, and failure replay together instead of trusting one successful lane snapshot by itself
  • treat the lane description as bounded authorization, not as a shortcut to stronger knowledge, recommendation, or lab claims

Open The Checked Artifacts

  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/runtime_run_registry.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/cross_family_run_bundle.json

Per-family artifacts:

  • dda:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dda/failure_replay.json
  • dia:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/dia/failure_replay.json
  • lfq:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/lfq/failure_replay.json
  • multiplex:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/multiplex/failure_replay.json
  • ptm:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/ptm/failure_replay.json
  • targeted:
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/run_bundle.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/stage_lineage.json
  • packages/bijux-proteomics-runtime/tests/fixtures/flagship_runs/targeted/failure_replay.json

Current Runtime Families

Workflow Runtime package id Current lane Execution mode
dda dda-maxquant-pipeline-corpus strict import lane over tracked MaxQuant exports import_only
dia dia-diann-pipeline-corpus raw-executable review lane over tracked DIA library-conditioned evidence raw_executable
lfq lfq-cohort-review-corpus raw-executable review lane over tracked feature and design tables raw_executable
multiplex multiplex-tmtpro-review-corpus raw-executable review lane over tracked channel feature and design tables raw_executable
ptm ptm-localization-review-corpus raw-executable review lane over tracked localization, feature, and FASTA evidence raw_executable
targeted targeted-transition-review-corpus raw-executable review lane over tracked targeted QC and follow-up artifacts raw_executable

What These Bundles Authorize

  • they authorize exactly the claim scopes listed in each run_bundle.json
  • they do not erase comparator refusal, thin grounding, or unjustified lab burden downstream
  • they keep the runtime stage lineage and failure replay story public instead of forcing readers to trust runtime prose

What Is Stronger Than Before

  • the runtime package now names one checked public bundle per workflow family instead of asking readers to reconstruct the live surface from fixtures alone
  • lane descriptions now make raw-executable and import-backed differences part of the public record
  • the registry is now one of the clearest places where operational depth in bijux-proteomics is visible without overselling what execution alone proves

Boundary

These bundles prove runtime execution and runtime traceability. They do not automatically upgrade knowledge, comparator, recommendation, or lab authority. Use the cross-family bundle to see those downstream owners directly.

When the question becomes how a lane should be reopened, challenged, or refused, continue with:

  • docs/09-bijux-proteomics-runtime/runtime-execution-boundary.md
  • docs/09-bijux-proteomics-runtime/black-box-run-verification.md
  • docs/09-bijux-proteomics-runtime/runtime-rerun-refusals.md