Coupling Constraints

[Aarush Garg]

Hello, I noticed in mgPipe, that when you run the flux variability analysis to obtain the min and max diet and fecal fluxes for the net secretion and uptake, It is ran on a coupling matrix called “A” rather than the stochiometric matrix S. I was hoping you could explain the reasoning behind setting the coupling matrix as the default parameter and where these constraints come from. Where do the rules that are held in model.C originate from? What is the significance of this? Thank you so much!

[Ronan M.T. Fleming]

See https://pmc.ncbi.nlm.nih.gov/articles/PMC9004645/

On Mon, 23 Jun 2025 at 02:52, Aarush Garg <aarushg...@gmail.com> wrote:

Hello, I noticed in mgPipe, that when you run the flux variability analysis to obtain the min and max diet and fecal fluxes for the net secretion and uptake, It is ran on a coupling matrix called “A” rather than the stochiometric matrix S. I was hoping you could explain the reasoning behind setting the coupling matrix as the default parameter and where these constraints come from. Where do the rules that are held in model.C originate from? What is the significance of this? Thank you so much!

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

Digital Metabolic Twin Center, www.digitalmetabolictwin.org

School of Medicine,
University of Galway.

Ireland.

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

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Peer-reviewed publications: https://goo.gl/FZPG23
Mobile:  +353 852 109 806
Github: @rmtfleming
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