mgPipe Community Model Infeasible

[Nicholas Y]

Hi,

I am trying to run community models using mgPipe. Some of my community models are becoming infeasible when I use the default community biomass constraints of [0.4, 1]. When I relax the lower bound constraint on the community biomass reaction to 0 for one such model, I see that the community biomass produces a nonzero flux, but it is less than 0.4.

I was wondering if you had any advice on the best way to handle situations like this? Would you recommend I relax the community biomass constraint? Or do I need to change my diet to ensure the models can produce a community biomass flux of at least 0.4? Do you have any recommendations for how I go about debugging this issue?

This issue occurs in a community simulation using standard AGORA2 models, which have been consolidated into pan models at the species level using MMT's createPanModels function.

Thank you for your time and assistance!

Best regards,

Nicholas Yousefi

[Almut Heinken]

Hi Nicholas,

you could indeed modify the required biomass through the lowerBMBound parameter. It depends on what kind of community is simulated and how much biomass production could be expected if that makes sense.

Alternatively, you could find out how the diet needs to be modified (might just be a single micronutrient that needs to be increased). To do that, you need to first relax the lower bound on biomass, then maximize biomass production for the community model in question. Investigate the shadow price to see if a particular metabolite has a nonzero value, indicating it limits biomass production.

I hope that helps.

Best regards,

Almut

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[Ronan M.T. Fleming]

Hi Nicolas,

in addition, one could try to find the minimal number of relaxations to make the model feasible

https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorial_relaxedFBABounds.html

Regards,

Ronan

To view this discussion visit https://groups.google.com/d/msgid/cobra-toolbox/CAKy8Drzosb9o1tPKKG1285Ltfv2OG-b0jjpMA_GLq_6D%3D1qNgA%40mail.gmail.com.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Digital Metabolic Twin Center, www.digitalmetabolictwin.org

School of Medicine,
University of Galway.

Ireland.

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