Containing Loops in Models

[Jason F]

Is one particular optimizing program (gurobi or tomlab cplex or other) better at containing loops in a models?  I am using gurobi, and despite not allowing loops in my call to optimizeCbModel, I still get these infeasible high flux loops that cause un-realistic results.  

Thanks in advance for any help,

Jason

[Jan Schellenberger]

Hi Jason,  Could you give some more details about what you are seeing?  In general, the choice of solvers should not make a difference.  If loops are off, there should not be any loops.  

I have seen flux distributions that are look like loops but aren't.  Loops do not have any exchange with the environment.  Another possibility is that the model is not mass/charge balanced and in this case the algorithm may not detect "loops" because mathematically they aren't loops.

-Jan

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[Ronan M.T. Fleming]

Hi Jason,
you can use checkStoichiometricConsistency.m to see if the model is
mass balanced.
Ronan

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[Jason F]

Jan and Ronan,

Thanks!  Despite trying to be really careful, I did discover some reactions that were not mass balanced. 

I first ran checkStoichiometricConsistency, and it did find it infeasible, but the m vector only pointed me to some metabolites that were simply dead ends.  Then I ran checkMassChargeBalance, and it found several rxns.  Not sure how I missed those, but thanks.

 I will make these corrections and hopefully, it will be corrected.  

Thanks again!

Jason

[Jason F]

Well, fixing the stoichiometric balance did not help.  After making several adjustments, and it passing both tests (checkStoichiometricConsistency and checkMassChargeBalance). It still has apparent loops.  I am not sure if it helps to provide perspective, but I including an image (produced by paint4net that includes fluxes above 3 units with the input carbon source set at 10).  Most of the high fluxes are > 100 units. I am at a loss.  Sorry.  Jason 

[Moritz Emanuel Beber]

Hi Jason,

On 07/25/2013 11:03 PM, Jason F wrote:

Well, fixing the stoichiometric balance did not help.  After making several adjustments, and it passing both tests (checkStoichiometricConsistency and checkMassChargeBalance). It still has apparent loops.  I am not sure if it helps to provide perspective, but I including an image (produced by paint4net that includes fluxes above 3 units with the input carbon source set at 10).  Most of the high fluxes are > 100 units. I am at a loss.  Sorry.  Jason

Have you tried parsimonious FBA? Check out the following paper:

Lewis, Nathan E, Kim K Hixson, Tom M Conrad, Joshua A Lerman, Pep Charusanti, Ashoka D Polpitiya, Joshua N Adkins, et al. 2010. “Omic Data from Evolved E. Coli Are Consistent with Computed Optimal Growth from Genome-scale Models.” Mol Syst Biol 6 (July 27). doi:10.1038/msb.2010.47. http://dx.doi.org/10.1038/msb.2010.47.

Basically, after a maximization of, for example, biomass, that value is fixed and all other fluxes are minimized, is that what you want?

Best,
Moritz