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known problems with linprog?

Anonymous
2011-08-04
2013-05-30

  • Anonymous
    2011-08-04

    I'm wondering whether there are known issues with linprog, Matlab's native linear programming solver. I saw that it is not supported by the toolbox, and I'm starting to understand why. I'm not able to use it on the outputs of readCbModel, while optimizeCbModel works fine. Is this a problem that is common? I've seen that others have this issue for other (non-systems biology) models, but I was wondering if this was typical of FBA models.

    See inputs below. Note that optimizeCbModel works (optimizing biomass production on aerobic glucose, iAF1260 xml file default), but linprog doesn't.

    >> ecoli=readCbModel('iAF1260.xml');
    >> optimizeCbModel(ecoli)

    ans =

               x:
               f: 0.7367
               y:
               w:
            stat: 1
        origStat: 5
          solver: 'glpk'
            time: 0.0940

    >> linprog(ecoli.c,,,ecoli.S,ecoli.b,ecoli.lb,ecoli.ub)
    Exiting: The primal is infeasible; the equality constraints are dependent
    but not consistent.

     
  • Daniel Hyduke
    Daniel Hyduke
    2011-08-04

    linprog doesn't work with the cobra toolbox.  if you look through the output of optimizeCbModel, you'll notice that it's using the 'glpk' solver - we provide binaries for glpk that work on some OSes so that's what's solving your problem not linprog.