i am new to modelling of cellular networks, and I have two basic questions, regarding the result interpration.

I am using the COBRAToolbox to do a flux balance analysis of a whole genome scale model of a bacteria. To get things started i replicated the results published in a paper, I have even been in correspondence with the author of the paper which happens to be the person who created the model i am using. So I am 100% sure that all the boundary conditions exchange fluxes and so on are as in the publication. I was able to reproduce this results and they match the experimental data.

The published results specifically mention the flux of a metabolite X of interest and compare the reaction rate of X to literature values and to laboratory experiments.

I did a FVA of X given all the boundaries, the soultion space is between 0 - 15 [mmol/g_dw/h], and the result when doing the FBA is aorund 7 [mmol/g_dw/h]? (I tried out multiple solvers, showing the same variation)

My questions:

  1. I understood the FVA as a analysis tool which shows me the possible solution space for a given flux , given a system with all limitations and boundaries.

So, how is the solver deciding which of the possible values are displayd, which heuristics are used?

  1. If the scattering for the possible solution space is so huge, what is the quality measure for this results?

Thanks in advance.

Best Regards

  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Apr 19, 2022 at 21:01


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