CUE on mixed C-Sources

[hgscott]

How does CUE differ when grown on two individual carbon sources vs when the media contains a mixture of the two? Run the mix with and without caFBA.

[hgscott]

I got the code for running caFBA from the supplementary MATLAB code from the Mori, 2016 paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004913

For now, I was using that E. coli model in the SI folder, because I knew it worked with caFBA.

I used the COBRA Toolbox to run plain FBA on a minimal glucose medium, minimal acetate medium, and a mix of the two (where the bounds were set so that the total carbon atom flux is the same). I didn't have a good way to plot the results, so I was just printing the fluxes for a few reactions to the screen.

I set up caFBA per the example in the SI code, but I am unsure if it is taking acetate into account properly, do I need to add another argument to this function:
https://github.com/C-CoMP-STC/fba-simulations-cue/blob/b74a56ba028a266077b00e3e244a13b7b5a1bdcb/ecoli_full/c_sources/mix/run_cobra_and_cafba.m#L87

[hgscott]

Daniel suggested before caFBA, one easier option is to constrain the total flux through the solution to below a certain threshold (like a more strenuous pFBA).

Also, Alvaro Sanchez;s group has implemented caFBA in COMETS, so maybe I could just use that.

[hgscott]

Look for "molecular crowding" for the constrained flux function in COBRA.

[hgscott]

Daniel said that Alvaro & Djorjie's new paper may have improved code for caFBA: https://academic.oup.com/mbe/article/40/9/msad187/7250431?login=true

[hgscott]

Daniel says to look at the epistatic interactions between CUE values. I.e. if you have CUE_{ACE} and CUE_{GLC} the CUE on the mixture is some function of both. Is it the mean, is it the sum, etc.?