Empty doubles when getting exchange reactions

[Catarina Ribeiro]

Hello,

I've been following the SteadyCom tutorial, and when it comes to getting the extracellular metabolites, the corresponding exchange reactions and the uptake rates of my community model, I get empty doubles and I don't get why.

I've attached the pipeline so far and the models i'm using.

Does anybody know what I may be doing wrong?

Thank you!

[Almut Heinken]

Hello Catarina,

the extracellular metabolites in the community model are in the "u" (lumen) compartment. If you are looking for the exchange reactions shared by both microbes, you need to look up the "u" tag.

metEx = strcmp(getCompartment(cm.mets),'u');

Also, this line

cm.mets = regexprep(cm.mets, '_([^_]+)$', '\[$1\]');

changes the metabolite IDs in the community model so I would recommend removing it.

Best,

Almut

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