From: James F. <fa...@pi...> - 2009-09-27 18:06:02
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Nicolas, Thank you for the clarification. I think I fully understood, although I will go through the example in more detail later to be sure. SpeciesTypes represent Entities that can have multiple binding sites and features. A bng "component" can be represented by an Entity with one binding site and one feature- a special case. I think that alleviates my concerns. Thanks, Jim Sent from iPhone bubo bubo On Sep 27, 2009, at 11:48 AM, Nicolas Le novère <le...@eb...> wrote: > James Faeder wrote: > >> I just wanted to throw my two cents in here. Bill is raising the >> same >> point that I brought up in our December, 2007 discussion, which is >> that there is some decoupling of structure and function that occurs >> when we separate binding sites and features. > > Just to nail it again. You can couple both. This is the role of the > speciesType. The only thing is that multi allows (but not force) > multiple > features associated with multiple binding sites. > >> enable us to make a one-to-one mapping between a BioNetGen model and >> its L3M encoding so that we can recover a BNG model from an L3M- >> encoded one. We could also achieve the same effect through BNG- >> specific annotations, > > If the model is generated by BNG in the first place, there is no > need for > annotation. It is sufficient to generate one speciesType per > component, > with one binding site, and, if needed, one state feature. It is only > when > exchanging models with other software that we may encounter problems. > HOWEVER, as we saw with the "core" SBML, guidelines and best practises > start to develop once people try to exchange models, and the > representations of different software progressively converge. > >> but I don't see a compelling reason to go that >> route, especially because Kappa and BNG both would require that same >> type of annotation. > > Do-we need multi to exchange models between BNGL and kappa? I was > under the > impression that a sed command would suffice ... ;-) > > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- > Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > +441223494521 > Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT > email) > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > > --- > --- > --- > --------------------------------------------------------------------- > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Sbml-multi mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-multi |