Skip to content

Arg-Met graph: scope obligate exchange and fluorescence noise to the tested reporter conditions #1431

Closed

Description

@realmarcin

Ecoli_K12_MG1655_Arg_Met_CrossFeeding_Coculture.yaml, PMID:42592155.

Keep both genotype-specific reciprocal exchange nodes and canonical NCBITaxon:511145 labels, without collapsing the two strains. Obligation holds under the tested amino-acid limitation; supplementation changes the interaction. The endpoint is single-cell fluorescent-reporter coefficient of variation, not directly resolved intrinsic transcriptional noise or universal protein-expression noise. Remove GO:0044419 interspecies annotation for these same-species strains. Preserve zero arrows while a separate source-backed mechanism expansion is researched; do not claim the expansion complete after node qualification. Keep the Arg-Trp and BL21/environmental-isolate experiments out of this two-strain graph.

Deduplication: 754 all-state issue titles/bodies, plus ignored/hidden-inclusive local review/research/history/tests/scripts/workflow search. Relevant #1164, #373, #1120 and #1121 read; #373 reused. Not every issue comment searched. No exact duplicate of these new findings in that scope.

Activity

  1. realmarcin commented on Oct 6, 2026

    @realmarcin
    ContributorAuthor

    Existing-graph defect addressed in #1437 at a22f0f8. Exact-head self-adversarial COMMENT: #1437 (review). 399 passed in 179.40s (0:02:59); actual post-commit docs-current passed. Three VFA arrows removed and two qualified; Arg/Met expansion remains pending under #1436. Close only after protected main merge. Other follow-ups remain open.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions