Question in Microbiome Modeling Toolbox -- Metabolites by Taxa Level Production

[Riddle0233]

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• Tried to solve the issue on my own
• Retried to run my code with the latest version of The COBRA Toolbox
• Checked that a similar issue has not already been opened

Hello,

I am working with the mgpipe function from the Microbiome Modeling Toolbox and would like to know the species/strains that produce the metabolites that are secreted out. My method is trying to find the metabolites that are secreted out and exist in lumen compartment (with reaction similar to 'h2[u] <=> panParabacteroides_merdae_h2[u] '), having a positive s*flux indicating production. The problem I am facing is I don't know how to extract the flux of reactions in each sample, as I have models for each sample as the output, which contains stochiomatric matrix but no flux values.

I am also asking to see if there are other more convinient methods to get the result?

Thanks a lot!

[rmtfleming]

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