How to calculate ATP yield in mol

[Joyssstan]

Hi,

I've just started to pick up cobra toolbox recently. While going through the supplementary example 2 from what is flux balance analysis? (http://www.nature.com/nbt/journal/v28/n3/abs/nbt.1614.html), the tutorial stated that the calculated maximum yield of ATP is 17.5 mol ATP/mol glucose.

I'm wondering what is the calculation involved in getting this value, 17.5 as the result from my simulation showed that the flux I have for ATPM is 182.5.

Can anyone help?

[kcwi...@colorado.edu]

I am having the same problem with trying to calculate the yield in moles too.  If you figured it out, could you help me?

[Priyanka Sadhukhan]

Hi,

I have never really tried the tutorials, but one way to go about computing the yield of a metabolite (mathematically) is that, you add a demand reaction and then maximize for it. Does the model have an exchange reaction (preferably extra-cellular) for atp? You can maximize that too. 

Hope this helps...

~ Priyanka Sadhukhan

On Fri, Jun 21, 2013 at 1:53 AM, <kcwi...@colorado.edu> wrote:

I am having the same problem with trying to calculate the yield in moles too.  If you figured it out, could you help me?

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~ Priyanka

[Abhishek Gupta]

Use E.coli core model (provided with COBRA toolbox)

Change Objective Reaction to 'ATPM'

Change Lower bound and Upper Bound to 0 and 1000 for 'ATPM'

Use OptimizeCbModel

Divide Objective function value with your Glucose Flux........

That's it :)

[kcwi...@colorado.edu]

I just got it!  The tutorial didn't say anything about the upper bound.  I'm a beginner, so I need everything spelled out for me :) Thank you!