Re: [cobra-pie] Phantom Exchange Reaction Returns?

[moritz...@gmail.com]

Hey Aimee,

I don't know how ModelSEEDpy works or doesn't work. Maybe your question is better raised with them? You say that the model is constructed with COBRApy underneath. So what happens if you run model.otpimize(), does it respect the bound change?

Best,

Moritz

On Fri, 2022-04-22 at 13:09 -0700, Aimee Kessell wrote:

Hi all,

I've been running a community model that uses CobraPy for the model with additional code from ModelSEEDpy and been having this odd situation:

I'm trying to change some exchange reaction bounds to push flux through the model, using:

model.reactions.get_by_id("RxnID").bounds = 0,0

I even check to make sure the reaction bounds is [0,0].

But when I try to run FBA on the community (using MSCommunity code from ModelSEEDpy), it runs as if the reaction bounds were never changed.

I know ModelSEEDpy is using CobraPy because if I change an inside reaction (not exchange), it keeps the change and runs with no issues. This only appears to be the case for exchange reactions.

Thoughts?

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[Daniel Farkas]

Hi Aimee, Moritz

I have the same issue using a community model with ModelSEED reactions. It was built with gapseq, then merged on kbase.

I encountered the exact same issue: the model.medium is not repsected by model.optimize().

Did you ever manage to solve this?

Many thanks,

Daniel