Zero flux when use two objective function

[Faezeh Zalpour]

Dear All,

I have a model for which I have defined another objective function in addition to biomass. But when I do the FBA analysis, the flux of one of the objective functions is zero, while it is not the case in the other model I have. I use solver glpk I use it. Can you help me to solve my problem please?

[Farid Zare]

Dear Faezeh,

Please provide details regarding your questions, such as the name of the model and the reactions that are set as the objective function. Please also consider that constraints, such as exchange reaction boundaries, may affect the flux distribution. Additionally, different models may exhibit various phenotypes and flux distribution values.

Regards,
Farid

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Farid Zare MSc

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Ph.D. Student at University of Galway, Ireland

Member of Recon4IMD & COBRA toolbox

Mobile: +353 87 490 1738

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GitLab: farid-zare

On Thu, 28 Mar 2024 at 12:47, Faezeh Zalpour <faezez...@gmail.com> wrote:

Dear All,

I have a model for which I have defined another objective function in addition to biomass. But when I do the FBA analysis, the flux of one of the objective functions is zero, while it is not the case in the other model I have. I use solver glpk I use it. Can you help me to solve my problem please?

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[Faezeh Zalpour]

Dear Farid,

I used the "iVS1191" model  (which is given in the article titled "High-quality genome-scale metabolic model of Aurantiochytrium sp. T66").
In addition to biomass, which is the main objective function with reaction number 1026, I set reaction number 939, which is related to DHA, and the reaction related to squalene (975) separately as the objective function, but in any case, I only have flux for biomass, and the flux is related to Squalane and DHA are zero.

Regards

Faezeh

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[Ronan M.T. Fleming]

Use https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialRelaxedFBABounds.html after sett a small lower bound on both objectives.

See section 2 of https://academic.oup.com/bioinformatics/article/39/9/btad450/7269197

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/CAKebX4xVgcwkOj_s5p5%3DAo5CoOt49u-m2pqfYpWKPH4Dbv_tgQ%40mail.gmail.com.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Associate Professor,
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University of Galway,

Ireland.

Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)

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