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Code Ocean validation record

This record separates observed platform execution from facts that have not yet been captured. A successful computation is not, by itself, an adapter release.

Validated execution-bearing commit

Field Evidence
Validation date 2026-10-01
Code Ocean capsule 5721592
Code Ocean computation 868130
Adapter commit 743acb2ebae0ca4325bf801bb8ef1f59a71ab3cb
Canonical module OMIX L2P Multi 4.1.0 at 53b2ca65aa23f54477f698c4ab6ce0d6ab637a5f
Runtime selected in Code Ocean OMIX Pathways (2); R 4.4.3, Bioconductor 3.20, fgsea, GSVA, l2p, l2psupp, and OmixPathwayPlots 0.2.0
Compute resource 1 core / 8 GB RAM
Effective demo input Attached Demo DEG_table; explicit DEG file left blank
Effective ordered comparisons B-A,C-A,B-C
Effective species and pathway collections Mouse; H, GO, REACTOME
Effective gene selection Threshold mode; p-value 0.05; absolute linear fold change 1.2
Effective shared-plot settings Top 20; adjusted-p-value significance; independent collection color scales
Observed outcome The synchronized computation completed successfully in 1 minute 26 seconds.

Observed artifacts

Code Ocean displayed the following /results artifacts for computation 868130:

  • l2p_multi_results.csv (11.75 MB);
  • l2p_multi_results_provenance.csv (2.03 KB);
  • L2P-Multi-Pathway-Bubble_across_collections.png (660.72 KB);
  • L2P-Multi-Pathway-Bubble_combined_pathways.png (672.15 KB);
  • L2P-Multi-Pathway-Bubble_go.png (526.76 KB);
  • L2P-Multi-Pathway-Bubble_h.png (412.77 KB);
  • L2P-Multi-Pathway-Bubble_reactome.png (642.72 KB);
  • L2P-Multi-Pathway-Bubble_manifest.csv (875 B); and
  • the captured run output (4.29 KB).

This verifies the attached-demo named-parameter run and the presence of the stable output set. It does not, by itself, verify the contents and ordering assertions inside every artifact.

Earlier computation

Computation 814585 completed successfully on 2026-09-30 against adapter commit f47e569dfc131bf38a47109b301d1772e03547f3 using OMIX Pathways v2. It preceded the documentation-only commits that recorded its evidence.

Evidence classification

This is partial platform validation. It confirms that exact adapter commit 743acb2ebae0ca4325bf801bb8ef1f59a71ab3cb could execute in Code Ocean with the named runtime and attached demo, and that the expected stable artifacts were produced. It does not establish the runtime's immutable digest, a published capsule release, the internal ordering assertions, or the remaining explicit-table, workflow, ambiguity, suffix-override, advanced-plot, and custom-pathway runs in the validation plan.

Remaining release gates

  • Capture the immutable digest for the exact Code Ocean runtime used.
  • Record any published platform release ID after explicit release approval.
  • Inspect the result and provenance tables plus bubble-plot manifest and record the required comparison-order, row-order, and scientific sanity assertions.
  • Complete the remaining explicit-table, workflow, ambiguity, suffix-override, advanced-plot, and custom-pathway cases in the validation plan.
  • Have Beacon verify the completed evidence record against the merged adapter.
  • Obtain explicit release approval before creating an adapter tag or publishing a capsule release.

Until those gates are complete, OMIX_MODULE_SOURCE.md must keep the adapter version, release tag, platform release, and runtime digest as Pending.