Closes #265: Make r_0446 (formate-tetrahydrofolate ligase) irreversible, to prevent non-zero flux through TCA cycle. (PR #290)
Features:
Add pathways responsible for the formation of hydrogen sulfide as well as other volatile sulfur compounds during fermentation (PR #300)
Closes #302: Simplify model curation with curateRxnsGenesMets function (PR #300)
Remove COBRA Toolbox and MATLAB-git dependencies for the MATLAB-based curation pipeline (PR #303)
Closes #308: Distribute yeast-GEM.mat in RAVEN's format, to include grRules and metComps fields (PR #301)
Refactor:
Change format of yeast-GEM.txt file to include metabolite names and compartments, instead of metabolite identifiers, to simplify diff-ing (metabolite identifiers are already trackable in the yml-file) (PR #312)
Main improvements in this PR:
r_0446
(formate-tetrahydrofolate ligase) irreversible, to prevent non-zero flux through TCA cycle. (PR #290)curateRxnsGenesMets
function (PR #300)yeast-GEM.mat
in RAVEN's format, to includegrRules
andmetComps
fields (PR #301)yeast-GEM.txt
file to include metabolite names and compartments, instead of metabolite identifiers, to simplifydiff
-ing (metabolite identifiers are already trackable in theyml
-file) (PR #312)I hereby confirm that I have:
main
as a target branch (top left drop-down menu)