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GapAnalysis

mvacher
2013-02-06
2013-05-30
  • mvacher
    mvacher
    2013-02-06

    Hi,
    I would like to use COBRApy to find and analyse gaps on SBML models. I was wondering if somebody had already ported the COBRA function in COBRApy ?
    I found "gapAnalysis.py" in the oven folder but it doesn't seem to be baked yet ;-)
    Is there any sample code to analyse gaps using COBRApy ?

    Thank you for your help,
    Regards
    Michael

     
  • Daniel Hyduke
    Daniel Hyduke
    2013-02-13

    Michael,

    I'm not sure how stable the gapAnalysis code is, but there's example code at the bottom of the python file: https://github.com/aebrahim/cobrapy/blob/master/cobra/oven/aliebrahim/gapAnalysis.py

    I'm not sure how detailed the examples or documentation are for gap analysis; I believe that Ali mostly coded them up so he could familiarize himself with the methods which is why it's not been baked.