fix: flux prediction through PPP about yeast-gem

[BenjaSanchez]

@hongzhonglu yes I encountered that when working in the GECKO project. I tried out some of Rui's suggestions from supp. table 4 but in the end only did 2 changes that solved the issue, as mentioned in the supplementary material of GECKO (section 3.2.1):
model = changeRxnBounds(model,'r_0245',0,'l'); %L-serine transport from mit to cyt
model = changeRxnBounds(model,'r_0659',0,'u'); %isocit + NADP -> 2-oxoglut + CO2 + NADPH
You could try with all of Rui's options or this one and see which model produces PPP flux. @zhengmingzhu should I create a new branch curation/fluxes for you to work on this?

[BenjaSanchez]

@hongzhonglu this issue should remain open until it is solved

[hongzhonglu]

@BenjaSanchez OK! Just want to make the tasks list simple. It is interesting that I heard that Yu didn't do any changes but still predicted well!

[BenjaSanchez]

@Yu-sysbio any insight on this?

[Yu-sysbio]

@BenjaSanchez I just used Yeast 7.6 to get flux distributions for Jianye's project and found increased fluxes through PPP pathway as growth rate increases. So Yeast 7.6 enables good flux predictions through PPP pathway in my cases.

[BenjaSanchez]

@Yu-sysbio which version of the model did you use for that? Downloaded straight from sourceforge? @hongzhonglu I think the current model here does not predict flux through PPP so before closing the issue we should show with some simulation script (that we can store in the repo) that the fluxes are active. As soon as we have memote working with the repo we could add said script to the list of tasks to check, right @Midnighter?

[Yu-sysbio]

@BenjaSanchez Yes, from sourceforge. I used the original version of Yeast 7.6 without any modifications.

[BenjaSanchez]

@Yu-sysbio thanks! Any additional constraints such as enforcing acetate/ethanol production? In a fully unconstrained model I did not see any PPP flux for the original model.

[Yu-sysbio]

@BenjaSanchez I just used experimental exchange fluxes (e.g. glucose, O2, CO2 for low growth rates, and glucose, O2, CO2, ethanol, acetate for high growth rates) as constraints and maximised growth. You can try it with Jianye's data.

[Midnighter]

As soon as we have memote working with the repo we could add said script to the list of tasks to check, right @Midnighter?

Currently, we can only run Python scripts. So you would have to construct a pytest test case and then configure memote to discover your custom test. Sounds more complicated than it actually is ;)

[BenjaSanchez]

@Yu-sysbio thanks for the guidelines, I'm sure they will be very helpful for @zhengmingzhu

@Midnighter I see. We can also later just translate it to Python, shouldn't be a problem. Will get back to you on the how-to later ;)