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genomic metabolic reconstruction

Hi,

I made a metabolic model using matlab. But it did not work when run FBA. So I try to figure out what is missing in the model. Then I found that there are 87 reactions that did not run, even all reactants are there.

Is there anyone know why the reaction did not run when all the reactants needed for it are there? and how can I fix this problem?

It is part of my master thesis, I'm stuck now, please give me some hints to do this guys.

Thanks

matlab metabolic-modelling genomic-reconstruction
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updated by Ram Ram • written by nhungptt17 • nhungptt17

Impossible to diagnose this without some attempt to show your code, and working environment...

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written by User 59 User 59

Hi Daniel Swan,

It is about the result of FBA optimizeCbModel when I apply it on my model. 

>> FBAresult=optimizeCbModel(nanno,'max')

FBAresult = 

           x: [956x1 double]
           f: 0
           y: [1086x1 double]
           w: [956x1 double]
        stat: 1
    origStat: 5
      solver: 'glpk'
        time: 0.0230

so f=0, no flux goes through my model. It is certaintly because of some gaps in the network. I'm making a metabolic network map by cytoscape to see what is the downstream and upstream of the gap reactions. But it is a little bit messy, so I wonder if there is any other way to find and fix the gap? or any other visualization tools which are easier to use

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updated by Ram Ram • written by nhungptt17 • nhungptt17

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