Final work discussion for this season

Had a great time presenting the design and implementation of CBMPy and how it can be used for model driven media design. Python, object-oriented programming, biochemistry, microbiology and algorithms all unleashed on an amazingly awake audience. Especially considering this happened the night before :-)

ICSB 2013 SBML3FBC and PySCeS CBMPy

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)
   

   cmod.createObjectiveFunction('R_biomass_reaction')

   
   


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

   cbm.CBSolver.analyzeModel(cmod)
   
   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')