Calculating Growth rates

[Bushra Saeed Dohai]

Dear Cobra group,

thanks for your unlimited supports, I am solving some tutorials for calculating the growth rate for the E.coli model, I followed the manual steps:

>> load Ecoli_core_model.mat;

>> model=changeRxnBounds(model,'EX_glc(e)',-18.5,'1');

>> model=changeRxnBounds(model,'EX_o2(e)',-1000,'1');

>> model=changeObjective(model,'Biomass_Ecoli_core_N(w/GAM)-Nmet2');

>> FBAsolution=optimizeCbModel(model,'max');

>> FBAsolution.f

ans =

    0.8739

According to the manual the value of the objective function should be 1.6531, I am trying to figure it out, your help is highly appreciated. Thanks

Sincerely,

Bushra Dohai Modelling Engineer and Research Technologist   Center for Science and Engineering NYU Abu Dhabi, United Arab Emirates Office Tel: +971 2 628 5144 P.O. Box 129188 http://nyuad.nyu.edu/research/centers-institutes/lab-algal-systems-biology.html

[Brandon Barker]

Is it possible you are using a different model or model version than what is found in the tutorial? 

[Bushra Saeed Dohai]

Dear Dr Brandon, 

Thanks for you reply yes I think I have the same version, I used the model that is in the cobra folder (testing->testmabs ), by the way even when I solved the  second example which is calculating the growth rate without Oxygen, still giving me the same answer (0.8739)!! so I can't get even different answers. 

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[richa...@gmail.com]

Hi,

In the commands you listed:

>> model=changeRxnBounds(model,'EX_glc(e)',-18.5,'1');

>> model=changeRxnBounds(model,'EX_o2(e)',-1000,'1');

are those the number 1 for the fourth entries?

I believe they are supposed to be 'l' (lower case L)

If the input is not 'u', 'l', or 'b', the script will do nothing.

Best,

Richard

[Bushra Saeed Dohai]

Hi, 

Yes Richard you are right, I put l (lowercase of L )instead of 1 ) since in Matlab  (l) appears as 1. I tried the substrates; ac,scald,akg,etoh,fru, and fum,  I got correct answers. 

however when I tried the glc-D the answer was 0 and I should get 1.7906, I don't know why!!! here is the matlab command:

>> load ecoli_core_model.mat

>> model=changeRxnBounds(model,'EX_glc(e)',0,'l');

>> model=changeRxnBounds(model,'EX_glc-D(e)',-20,'l');

>> model=changeObjective(model,'Biomass_Ecoli_core_N(w/GAM)-Nmet2');

>> FBAsolution=optimizeCbModel(model,'max');

>> FBAsolution.f

ans =

     0

I highly appreciate your help Cobra Group

[Sung Yoon]

If you look at the rxnNames, you can see that glc-D (D-Glucose) is actually referring to the 'EX-glc(e)' reaction and there is no separate 'EX_glc-D(e)' reaction.

Try:

>> load ecoli_core_model.mat

>> model=changeRxnBounds(model,'EX_glc(e)',-20,'l');

>> model=changeObjective(model,'Biomass_Ecoli_core_N(w/GAM)-Nmet2');

>> FBAsolution=optimizeCbModel(model,'max');

>> FBAsolution.f