a question about FBA objective function

[Payam Setoodeh]

Dear COBRA group,

I was wondering if anyone could possibly let me know how I can consider the objective function as maximization of ATP production per flux unit, instead of biomass in a metabolic network. Frankly speaking I have problem in writing the corresponding codes. i should mention that I use cobra 2.0.4 and MATLAB coding.

Any suggestion would be greatly appreciated.

Best Regards

Payam Setoodeh

[Rohit Vashisht]

Hi

This can be done by maximizing for ATP maintenance reactions in your model.  

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Regards
Vashisht

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[Payam Setoodeh]

Dear Rohit,

Thank you very much for your help and quick reply. I mean that I do not know whether i should consider a virtual exchange flux for ATP or not.

Also, I do not know how i can calculate all fluxes in order to calculate the mentioned objective function.

Moreover, I was wondering if you could possibly let me know which solver should be employed for this aim. 
i greatly appreciate anybody's help.

Best Regards

Payam

[Rohit Vashisht]

Dear Payam

I guess we can introduce an ATP maintenance reaction by computing for all the reactions that produce and consume ATP and then maximize it, I am not sure though but that's how we go about max ATP globally unless until asked otherwise.
Regarding solver, since it can be solved using LP therefore either Lindo or Cplex should be good.

Sent from Vashisht's Lumia

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From: Payam Setoodeh
Sent: 27-04-2012 10:12
To: cobra-...@googlegroups.com
Subject: Re: a question about FBA objective function

[Alyaa Mahmoud]

Dear Payam

Please check my reply below, I write in red. 

>> I was wondering if anyone could possibly let me know how I can consider the objective function as maximization of ATP production per flux unit, instead of biomass in a metabolic network -> you can add an ATP demand reaction to your model, however, I learnt that its not very meaningful if we just use ATP maximization as ATP objective function. 

>> Frankly speaking I have problem in writing the corresponding codes. i should mention that I use cobra 2.0.4 and MATLAB coding.

Any suggestion would be greatly appreciated -> I paste my code below which I used to use before. 

% add ATP demand reaction to your model 

model = addReaction(model, 'ATP_objective', 'atp + h2o -->  adp + h + pi')

%Change objective function to ATP maximization

model=changeObjective(model, model.rxns, 0); 

model=changeObjective(model, 'ATP_objective',1);   

sol=optimizeCbModel(model, 'max');

>>I guess we can introduce an ATP maintenance reaction by computing for all the reactions that produce and consume ATP and then maximize it, I am not sure though but that's how we go about max ATP globally unless until asked otherwise. -> you can alternatively add a consumption reaction for ATP exactly as Vashishtrv mentioned; 

model = addReaction(model, 'ATP_objective', 'ATP --> ')

again, I am not sure about the biological significance of using ATP maximization as the objective function :S 

Good luck

yours, 

Alyaa 

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Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare