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Fails after restart

Anonymous
2012-10-19
2013-05-30

  • Anonymous
    2012-10-19

    HI,

        I have my libSBML and COBRA installed and everything seems perfect at first. But problems occurs once I restart Matlab.

        When testAll, I got:

    Tests passed:
    testElementalBalance
    testModelManipulation
    testSBML

    Tests not passed:
    testBuildMPS
    testC13Fitting
    testDeletionStudy
    testFBA
    testFVA
    testGDLS
    testGrowthExpMatch
    testMOMA
    testMaps
    testOptKnock
    testRobustnessAnalysis
    testSampleCbModel
    testgpSampler
    testSolvers
    testTissueModel
    testpFBA

        However, I just run initCobraToolbox.m again and things get back to normal. So I think there may be some problems when the installing scripts try to make some environmental settings permantly in Matlab.

        Oh, I am on Win7 x64, with Matlab 2011b, libSBML 5.6.0, COBRA 2.05.

        Can anyone help me? Thanks a lot!

     
  • Daniel Hyduke
    Daniel Hyduke
    2012-10-19

    Basically, the way things work with the COBRA Toolbox is that some parameters, such as solvers and paths need to be set in order for it to run correctly.  After running initCobraToolbox you can have matlab save the new paths by typing save path; however, to get matlab to initialize the solvers so that you don't have to run initCobraToolbox will require you to have a startup.m file (http://www.mathworks.com/help/matlab/ref/startup.html) where you set the specific solvers that you have installed.

     

  • Anonymous
    2012-10-20

    daniel,

    So, that means initCobra still need to be run every time I launch Matlab, though not manually… All right… after all I get to know where the problem is.
    Thank you, daniel.