Small core SBML L3+FBC model published in Biotechnology Journal

The first SBML3+FBC model (a small core model) published in support of this paper:

Basic concepts and principles of stoichiometric modeling of metabolic networks

Timo R. Maarleveld, Ruchir A. Khandelwal et. al

Biotechnology Journal, Volume 8, Issue 9, pages 997–1008, September 2013

 

Generic annotation in constraint based models

During COMBINE 2013 Frank and myself tried to come up with a compromise proposal that would combine the best elements of the two current "generic annotation" proposals that are under discussion.

When we presented this at COMBINE 2013 it was well received by the members of the community that attended the FBC session. For background on this discussion please see this document.

We call this proposal AdditionalProperties and an initial specification can be found here.

COMBINE 2013 presentations

It was really fantastic to leave a great meeting like COMBINE in Paris and fly straight to South Africa for a vacation. I'll post some vacation pictures elsewhere but for now here are links to my presentation and the slides I made while chairing the FBC session.

A short presentation: Modelling at genome scale: introducing the SBML3 FBC package

And some technical stuff on a new proposal for generic annotation and a formal UML description of the gene association extension discussed during HARMONY 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)
   

   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')