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Update ORNL trophic-model edges using full text and bound modeled flux allocations #1646
Description
CommunityMech:000176; DOI:10.1186/1471-2180-10-149 and PMID:22319433. Exact-system full primary text is now available and read, making the old inaccessible-full-text discussion stale. Preserve both cross-feeding arrows and measured bulk chemistry; individual exchange allocations and hydrogen/ethanol partition are model estimates, not resolved tracer flux. Replace reciprocal SYNTROPHY and NICHE_PARTITIONING overclaims; correct graph fumarate grounding. OptCom assumptions are computational and its fourth-member extension is not this system. Close only after protected-main merge.
Dedup:926 all-state issue titles/bodies, 99 ignored/hidden-inclusive local matches (excluded git/docs/site/reference cache). Read matching12/416/592/595/1083/1532/1533 plus529/543. No exhaustive PR-comment audit. Source-based self-adversarial review, not independent approval.
Activity
realmarcin commentedon Oct 7, 2026
Addressed in #1651 at d9da91d; exact-head self-review:#1651 (review). 696 passed in 202.21s (0:03:22); post-commit docs-current passed. Every-node/every-arrow decisions and actual output digests committed. Not independent approval; close only after protected-main merge. Metadata #1650 remains unfinished; all four current reference gates passed.