06 March 2013

Recon 2 translated to SBML Level 3 with FBC

Yesterday I translated the newly released Human metabolic map Recon 2 from its existing COBRA format into SBML 3 with FBC. The model is now available from cbmpy.sourceforge.net

It turned out to be trivial, here's what I did:

  1. Downloaded the model from biomodels

  2. Loaded it into CBMPy, this translates the model into SBML3+FBC using libSBML 5.8.0

    cmod = cbm.CBRead.readCOBRASBML('MODEL1109130000.cobra.xml', os.getcwd())

  3. At this point there is no objective function defined so I created one (R_biomass_reaction)

  4. All that's left is to solve it:

    INFO: Model is optimal: 1
    Solution status = 1 : optimal
    Solution method = 2 : dual
    Objective value = 100.0
    Status: Model is optimal

  5. As this is a rather large model I decided to try my multicore FVA and see what happens (I decided to use two processing threads on  a quad core CPU). This took about and hour in the end which is slow, but this is a good excuse to look at some of the newer optimized FVA algorithms out there.
    fvadat = cbm.CBMultiCore.runMultiCoreFVA(cmod, procs=2)

  6. Finally I want to write the whole model, the FBA solution and FVA results to file. Excel 97 is actually quite a good format for this, next step is a COMBINE archive.
    cbm.CBWrite.writeModelToExcel97(cmod, 'results.xls')


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