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…ator The model is built by Human-GEM's code/animalGEM/generateAnimalGEM.py, which replaces masterScriptZebrafishGEM.m: orthology-based draft from Human-GEM 2.1.0, species-specific network, gap-filling of the essential tasks, and the version and date stamped into the model metadata. The files move to the RAVEN 3 YAML layout written by raven-toolbox, so this diff is large.
…ed reactions The generator now pins each degenerate minimum-cost fill to the fewest, lowest-id reactions, so the gap-filled set no longer depends on the solver and the MATLAB and Python generators give the same model. Gap-filled reactions keep their Human-GEM notes, with "reaction added by gap filling" appended.
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Updated: the generator now resolves gap-filling ties (fewest, lowest-id reactions), so the gap-filled set no longer depends on the solver, and the MATLAB and Python generators give the same model. Gap-filled reactions also keep their Human-GEM notes. This changes a few gap-filled reactions. |
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Main improvements in this PR:
Regenerates Zebrafish-GEM from Human-GEM release 2.1.0 with the Python generator
code/animalGEM/generateAnimalGEM.pyin Human-GEM (SysBioChalmers/Human-GEM#1141), which replacesmasterScriptZebrafishGEM.m.Depends on SysBioChalmers/Human-GEM#1141: the README and
code/README.mdpoint to the generator, which is on that branch until it is merged.MAR00021. For Human-GEM 2.0.0-2.1.0, the cofactor poolMAR00022uses lipoic acid instead of[protein]-N6-(lipoyl)lysine, which nothing produces (CurateMAR00021(biomass objective of the animal GEMs): it is infeasible in v2.0.0-v2.1.0 Human-GEM#1140); this is noted on the reaction.model/Zebrafish-GEM.{yml,xml,mat},model/reactions.tsv,model/metabolites.tsv,version.txt, README counts,code/README.md;code/masterScriptZebrafishGEM.mremoved.Large diff. The files move to the RAVEN 3 YAML layout written by raven-toolbox, and
reactions.tsv/metabolites.tsvare no longer quoted, so nearly every line changes. The content changes come from the new template (Human-GEM 2.1.0) and are not reviewable line by line.Tested. The same generator run on Human-GEM 1.18.0 reproduces the committed Mouse-GEM 1.8.0 exactly (12987 reactions, 2846 genes, identical gene sets). This build passes the essential metabolic tasks with
MAR00021as the objective (Gurobi); SBML and MAT files read back with the same reaction count.I hereby confirm that I have: