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Adding a number to the group association will duplicate multistate multicomponent extension and still may require explanation. Totals of entities can be easily computed through functions over members of groups. If more information is required (like number of phosphogroups in home- and hetero-dimers), the only proper solution would be to use multi-state multi-component extension. I believe groups in the core are necessary as supplement to functions and rules. I hope that people requesting speciesTypes can be satisfied with groups. And, because groups are not used in simulations, extra burden on software tools will be minimal.

Michael
______________________________________
Michael Blinov
Assistant Professor
Center for Cell Analysis and Modeling
University of Connecticut Health Center
http://www.ccam.uchc.edu/mblinov/ <http://www.ccam.uchc.edu/mblinov/>

________________________________

From: sbml-discuss-bounces@caltech.edu on behalf of Chris J. Myers
Sent: Wed 9/9/2009 6:30 PM
To: SBML Discussion List
Cc: SBML Discussion List
Subject: Re: [sbml-discuss] Proposed addition to L3 core



This is why I suggest adding a number to the group association. So
you could have a group CIt with species CI and CI2. CI would be
associated with group CIt with value 1 and CI2 would be associated
with group CIt with value 2.

Chris

Sent from my iPod

On Sep 9, 2009, at 1:13 PM, "Michael Hucka" <mhucka@caltech.edu> wrote:

> myers> I'm not sure though how strongly I would push to
> myers> have such a concept in the core. I would not argue
> myers> against it, since it is useful. If this idea is
> myers> absorbed into the groups package, then I would like
> myers> to see it modified to accept a number which can be
> myers> interpreted as the number molecules in a complex as
> myers> described above.
>
> Hi Chris,
>
> Although this is an attractive idea, there is a significant
> problem in coming up with a universal way of counting the
> entities (or summing the amounts of all the species). Your
> example didn't involve a simple sum of X = A + B + C ...,
> but multipliers (X = A + 2B ...), which means there must be
> a scheme for people to express exactly how they want things
> counted up. That in turn means arbitrary formulas. Where
> would such formulas go, and how would it differ from using
> parameters and assignment rules today? (I'm not being
> dismissive here, just trying to think the ideas through.)
>
> MH
>
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