'Infeasible' results from simulatePairwiseInteractions

[majunyeong]

I am trying to predict interactions between microbes using the simulatePairwiseInteractions function with my models created through CarveMe.
I modified the 'HighFiberDiet_Oxygen' condition provided in the tutorial ("https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialMicrobeMicrobeInteractions.html") to fit my model.

my_dietConstraints_240102.txt
(ex) EX_fuc_L[u] --> EX_fuc__L[u] (BiGG format)

However, I got the following result:

Most of the results were 'Infeasible'. Even more confusing, some pairs used the same diet and got normal results like 'Parasitism' or 'Amensalism', while others got results like 'No_Result'.

I have found the following similar issue, which has not been resolved
: #2009

I also checked to make sure that the exchange functions I put in as dietConstraints in the paired models I used for testing existed for the most part. I found that on average, about 52% of the exchange functions in the dietConstraints are present in the paired model. When I did the same analysis using the AGORA models and the dietConstraints from the tutorial, I found that on average about 60% of the exchange functions in the dietConstraints were also present in the AGORA paired model. The problem didn't seem to be caused by the dietConstraint I modified not being recognized by my paired models.

How can I solve this problem?

I hereby confirm that I have:

• 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

(Note: You may replace [ ] with [X] to check the box)

[rmtfleming]

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

…

On Wed, 10 Jan 2024 at 11:25, majunyeong ***@***.***> wrote: I am trying to predict interactions between microbes using the simulatePairwiseInteractions function with my models created through CarveMe. I modified the 'HighFiberDiet_Oxygen' condition provided in the tutorial (" https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialMicrobeMicrobeInteractions.html") to fit my model. my_dietConstraints_240102.txt <https://github.com/opencobra/cobratoolbox/files/13886550/my_dietConstraints_240102.txt> (ex) EX_fuc_L[u] --> EX_fuc__L[u] (BiGG format) However, I got the following result: infeasible_result.png (view on web) <https://github.com/opencobra/cobratoolbox/assets/87792306/2acd57ed-b4db-4652-bc26-9b06bd1b0111> Most of the results were 'Infeasible'. Even more confusing, some pairs used the same diet and got normal results like 'Parasitism' or 'Amensalism', while others got results like 'No_Result'. I have found the following similar issue, which has not been resolved : #2009 <#2009> I also checked to make sure that the exchange functions I put in as dietConstraints in the paired models I used for testing existed for the most part. I found that on average, about 52% of the exchange functions in the dietConstraints are present in the paired model. When I did the same analysis using the AGORA models and the dietConstraints from the tutorial, I found that on average about 60% of the exchange functions in the dietConstraints were also present in the AGORA paired model. The problem didn't seem to be caused by the dietConstraint I modified not being recognized by my paired models. How can I solve this problem? *I hereby confirm that I have:* - 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 *(Note: You may replace [ ] with [X] to check the box)* — Reply to this email directly, view it on GitHub <#2213>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQMEOUPXCP6TWNSMEXCK43YNZ3DZAVCNFSM6AAAAABBUT34AOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TIMJWGIZDSOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D. ---------------------------------------------------------------------------- Associate Professor, School of Medicine, University of Galway, Ireland. Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD <https://www.recon4imd.org/>) ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Github: @rmtfleming <https://github.com/rmtfleming> ----------------------------------------------------------------------------

[almut-heinken]

Hello,
do the individual models (without joining them) grow on this diet? You may have to add additional compounds to enable growth.
Best regards,
Almut