Interpretation of Subsystem Abundance

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Ari Ufondu

Apr 4, 2023, 1:10:13 PMApr 4
to COBRA Toolbox
Dear community,

I have been using the mgpipe toolkit for the simulation of microbiome communities comprised of genome-scale models. It has been going well, but I am struggling with the interpretation of some of the results.

One of the main outputs is a 'SubsystemAbundance.csv' file. I think I understand the general gist of it, but can someone please explain exactly what the output is in the simplest terms? Specifically, what is the program calculating to come up with the numbers under each subsystem for each sample? 

Thank you very much in advance!


Almut Heinken

Apr 7, 2023, 10:45:39 AMApr 7
Dear Ari,
the subsystem abundance is calculated in this function:
It is the relative abundances of all reactions in this subsystem summarized for one microbiome sample. So if the subsystem abundance was 1, all reactions in this subsystem present in at least microbiome would be in this microbiome sample each with a relative abundance of 1.
I hope that makes things more clear.
Best regards,


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