what means FBA?

[roohallah]

Hi everyone

I've recently started working with COBRA toolbox.So I do not have enough information about it. I am an amateur.

I'll appreciate if you can help me.

My goal is to reconstruct the network of cyanobacteria metabolism. So that these cyanobacteria to produce biofuel.

So I did the following steps:

 

1) I enter SBML file into COBRA toolbox by this code:

> > model  = readCbModel([ filename])

 

2) I added the desired reactions by this code:

> > [model]  = addReaction(model, rxnName, metaboliteList, stoichCoeffList, [revFlag], [lowerBound], [upperBound], 

[objCoeff], [subsystem], [grRule], [geneNameList], [systNameList], [checkDuplicate])

 

3) I performed flux balance analysis by this code:

> > [solution]  = optimizeCbModel(model)

 

4) The following results were obtained:

x: [3466x1 double]

f: 333.3333

y: [1537x1 double]

w: [3466x1 double]

stat: 1

origStat: 5

solver: 'glpk'

 time: 1.0570

As you can see F=333.333

What is interpretation of F=333.333?

Whether the results are acceptable?

Is the flux units (mmol / g / h)?

The network is able to produce biofuel?

Is my solution correct? Or is there something wrong?

Thank you for your attention

Regards

 

 

 

 

[eve kuhestani]

file://localhost/D:/thesis/New%20folder/web%20pages/What%20is%20flux%20balance%20analysis%20cobra%20toobox.htm
hi. check out this article
and have a look at COBRATool box protocol . you can find its article
easily search it in google

On 9/7/13, roohallah <roohal...@gmail.com> wrote:
>
>
> *Hi everyone*

>
> I've recently started working with COBRA toolbox.So I do not have enough
> information about it. I am an amateur.
>
> I'll appreciate if you can help me.
>
> My goal is to reconstruct the network of cyanobacteria metabolism. So that
> these cyanobacteria to produce biofuel.
>
> So I did the following steps:
>
>
>

> *1) I enter SBML file into COBRA toolbox by this code:*

>
>> > model = readCbModel([ filename])
>
>
>

> *2) I added the desired reactions by this code:*

>
>> > [model] = addReaction(model, rxnName, metaboliteList, stoichCoeffList,
>> >
> [revFlag], [lowerBound], [upperBound],
>
> [objCoeff], [subsystem], [grRule], [geneNameList], [systNameList],
> [checkDuplicate])
>
>
>

> *3) I performed flux balance analysis by this code:*
>
>> > [solution] = optimizeCbModel(model)
>
>
>
> *4) The following results were obtained:*
>
> *
> *
>
> *x: [3466x1 double]
> *
>
> *f: 333.3333
> *
>
> *y: [1537x1 double]
> *
>
> *w: [3466x1 double]
> *
>
> *stat: 1
> *
>
> *origStat: 5
> *
>
> *solver: 'glpk'
> *
>
> * time: 1.0570*
>
> *
> *
>
> *As you can see F=333.333*
>
> *What is interpretation of F=333.333?*
>
> *Whether the results are acceptable?*
>
> *Is the flux units (mmol / g / h)?*
>
> *The network is able to produce biofuel?
> *
>
> *Is my solution correct? Or is there something wrong?*
>
> *
> *
>
> *
> *
>
> *
> *
>
> *
> *
>
> *Thank you for your attention*
>
> *Regards*
>
> * *
>
> * *
>
> * *
>
> * *
>
> --
>
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>

[roohallah]

hi dear eve

I have fully read the two articles:

1- What is flux balance analysis?(Supplementary Tutorial)

2- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

They were very helpful and informative

I found answers to many questions

But I have a major problem.

I've run the following codes:

changeCobraSolver('glpk')

model = readCbModel('BMID000000140884')

model = changeRxnBounds(model,'dioxidocarbon',0,'0')

model = changeRxnBounds(model,'o2',0,'0')

FBAsolution = optimizeCbModel(model,'max')

But again, the flux was 333!

The cell grows 333 times in one hour!

I do not understand why!

Can anyone help me?

FBAsolution = 

           x: [3464x1 double]

           f: 333.3333

           y: [1535x1 double]

           w: [3464x1 double]

        stat: 1

    origStat: 5

      solver: 'glpk'

        time: 0.2120

[Chris Gowen]

Hi Roohallah,

I believe that when you use changeRxnBounds, you need to specify the reaction id (i.e. "C00011_in") rather than the reaction name (i.e. "dioxidocarbon_in"). It looks like you may not be setting the boundary conditions you think you are. If you still have problems, it might be helpful to see the output of printUptakeBound(model).

Chris

--

[roohallah mahdi]

hi dear chris

Many thanks for your help.

As you said, I run my code But again, the f = 333.333

model = readCbModel('BMID000000140884');

>> model = changeRxnBounds(model,'C00011_in',0,'0')

FBAsolution = 

           x: [3464x1 double]

           f: 333.3333

           y: [1535x1 double]

           w: [3464x1 double]

        stat: 1

    origStat: 5

      solver: 'glpk'

        time: 0.2370

When I run the code

printUptakeBound(model)

Answer was:

printUptakeBound(model)

ans =

   Empty matrix: 0-by-1

You'd be very grateful if you help me

Regards

[Ines Thiele]

Hi Roohallah

the correct syntax of the command changeRxnBounds is

model = changeRxnBounds(model,rxnNameList,value,boundType)

with boundType being 'l' (its a small L) for lower, 'u' for upper and 'b' for both

consequently your command should read

model = changeRxnBounds(model,'C00011_in',0,'u')

to get the syntax of a COBRA command, type, e.g.,

help changeRxnBounds

best Ines

Ines Thiele, Ph.D.

Associate Professor in Systems Biomedicine

Head of the Molecular Systems Physiology Group

Luxembourg Centre for Systems Biomedicine 

UNIVERSITY OF LUXEMBOURG

CAMPUS BELVAL

7, avenue des Hauts-Fourneaux

L-4362 Esch-sur-Alzette

Luxembourg

www.lcsb.lu 

thielelab.eu 

GoogleScholarProfile

--

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[roohallah mahdi]

hi dear Ines

I run bellow codes:

>>changeCobraSolver('glpk');

>> model = readCbModel('BMID000000140884');

>> model = changeRxnBounds(model,'C00011_in',0,'u')

But again, the following result is obtained

FBAsolution = 

           x: [3464x1 double]

           f: 333.3333

           y: [1535x1 double]

           w: [3464x1 double]

        stat: 1

    origStat: 5

      solver: 'glpk'

        time: 0.3510

I'm totally confused

Please help me. To obtain the correct result for me is very important and necessary.

Regards

[Ines Thiele]

Hi

there are 2 possibilities

either your change in bounds has no effect on objective value, and/or the model constraint is not set correctly. To check if you correctly set your desired reaction to an upper bound of 0 please type:

model.ub(strmatch('C00011_in',model.rxns,'exact'))

Ines

[roohallah mahdi]

i run bellow codes:

>> changeCobraSolver('glpk');

>> model = readCbModel('BMID000000140884');

>> model = changeRxnBounds(model,'C00011_in',0,'u');

model.ub(strmatch('C00011_in',model.rxns,'exact'))

ans =

   0

[roohallah mahdi]

Mrs. Ines

Aside from the two papers,

1- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 

2- What is flux balance analysis? Supplementary Tutorial

Is there other easier and clearer to teach COBRA toolbox?

I'm an amateur, so I need a good educational resource to learn all the techniques of COBRA toolbox.

Many thanks for your helps.

Regards