New biomass #174
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New biomass #174
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* upload new biomass composition in physiology/biomassCompsition_Cofactor_Ion.tsv * upload ion related exchange and transport rxns
* update all functions related to the change of new biomass * upload the function of AddCofactorIon.m
run scaleBiomass will update the model with new biomass composition.
BenjaSanchez
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Nov 5, 2018
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@feiranl below some comments, most of them are for complying with style or errors in the code due to added paths in your Matlab session. Note that as this is a rather larger update, it will be merged to devel after the next yeast 8.3.2 release, so this will go into yeast 8.3.3.
ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv
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* update coefficients for NADH/NADP/NADPH/NAD
* change one rxn name to keep consistency
* fix the cd problem in the function * fix a bug for rerun the function
rerun the function ScaleBiomass * update the confidence score to be 2 for those rxns which have GPRs * update coefficients for NAD/NADH/NADP/NADPH
corret the reference for 9 ions
delete unused variables
BenjaSanchez
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Nov 8, 2018
ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsv
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BenjaSanchez
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* change function name to avoid misleading.
BenjaSanchez
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Nov 16, 2018
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Nov 26, 2018
PR #174 included "cofactor" & "ion" pseudo-metabolites, so addSBOterms.m should be modified accordingly
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Main improvements in this PR:
ComplementaryData/physiology/biomassComposition_Cofactor_Ion.tsvI hereby confirm that I have:
develas a target branch (top left drop-down menu)