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Whole-cell modeling forum • View topic - Procedure to generate a COBRA compatible submodel?

Procedure to generate a COBRA compatible submodel?

Forum for getting started whole-cell modeling

Procedure to generate a COBRA compatible submodel?

Postby bebarker » Wed Apr 22, 2015 11:09 am

bebarker
 
Posts: 2
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Re: Procedure to generate a COBRA compatible submodel?

Postby jonrkarr » Wed Apr 22, 2015 12:16 pm

The only sub-model which uses constraint based modeling is the metabolic sub-model. The other sub-models use different mathematical formalisms which aren't compatible with COBRA.

We do use the COBRA toolbox to output this sub-model to SBML (see: ). The SBML file is available at .
jonrkarr
 
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Joined: Fri Feb 06, 2015 7:56 pm

Re: Procedure to generate a COBRA compatible submodel?

Postby bebarker » Wed Apr 22, 2015 1:47 pm

Thanks - I appreciate the pointers and quick response (and also the fact that it is already a supported feature!), will try it out starting today.
bebarker
 
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