yeast 8.3.3 #182
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yeast 8.3.3 #182
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to comply with sysbio rulebook
* 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.
* 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
* change function name to avoid misleading.
New biomass
"malate/β-methylmalate synthase", introduced in PR #156, creates parsing errors -> now it's stored as "malate/beta-methylmalate synthase"
PR #174 included "cofactor" & "ion" pseudo-metabolites, so addSBOterms.m should be modified accordingly
Fix/biomasSBOterms
fix: non-compliant symbol
fix: keywords
Doc/citation guidelines
BenjaSanchez
added
the
new release
Add a title for the data file
Add a exchange reaction for Ca 2+
change the function to let Ca2+ can enter into the cell freely update in the model
hongzhonglu
approved these changes
Dec 5, 2018
|
@hongzhonglu even though there are many commits included, the model did not change significantly (less than 15 rxns), compared to e.g. release 8.3.0, where >200 rxns were added. I think increase to 8.3.3 is better suited, based on our contributing guidelines. |
… update fix the rxnconfidence scores for those reactions in this update:exchange reactions: NAN; reactions for modeling: 1
Fix biomass: Add Ca(2+) into Biomass
for new release
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cofactor pseudoreactionandion pseudoreaction) added to the model as extra requirements to the biomass pseudoreaction (PRs New biomass #174 & Fix biomass: Add Ca(2+) into Biomass #183).addSBOterms.madapted to identify new pseudoreactions (PR Fix/biomasSBOterms #180).