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Hello, I am working with a micom.community model of two bacteria and not quite sure how to understand the output of the tradeoff function: SA_SE_community.cooperative_tradeoff(fraction=0.8, fluxes=True, pfba=True) I accessed the fluxes and displayed them and the dataframe looks like this: Does the general rule hold that negative fluxes represent import, i.e. S. epidermidis consumes for example alanine?
I would have assumed that both organisms use the community compartment m, but for some reason, this is only used by S. aureus and the medium. Conversely, e.g. in EX_cl_e, both organisms have fluxes, whereas the medium uses the _m flux. Would be great if someone could help me understand this :) |
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Hi, You are right that the default direction for exchanges in AGORA is export, so negative fluxes denote imports. This doesn't have to be true in general though. You can check by looking at NaN means the reaction is absent in this organism/compartment. It's a bit hard to tell but the exchanges ending in For chlorine having all fluxes negative just means that it enters the system at a particular flux and is imported by both taxa, so that makes sense. FWIW I also think this format for fluxes is a bit hard to understand. My plan is to change it to something more like the |
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Hi,
You are right that the default direction for exchanges in AGORA is export, so negative fluxes denote imports. This doesn't have to be true in general though. You can check by looking at
community.reactions.EX_cl_e__iYS854.reaction
for instance to verify.NaN means the reaction is absent in this organism/compartment.
It's a bit hard to tell but the exchanges ending in
_e
are exchanges for individual bacteria, whereas exchanges ending in_m
are imports and exports in the environment or medium. So those are never associated with any taxon. So for instance for alanine, the molecule is entering the extracellular space at a flux of 2.28. All of this is imported by S. epidermis. You see a hi…