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Hi All--

Hi--

Michael B's ideas recall a thought I had while Mike H was presenting the
Group package last week. If we were to allow group IDs in the reaction
definition (as reactants or products and in the kineticLaws), this could
address many of the problems in re-defining reactions in multiple
compartments (thus overlapping with Arrays), because we could re-use the
same kineticLaw for all reactions involving the group elements. It also
makes contact with the discussion on generics, though leaving open the
problem of providing an appropriate mapping from generic reactants to
generic products. In fact, it seems it might cause more problems than it
solves, from which we might take the lesson: keep the Groups very
simple, superficial, and vanilla, lest they come back and bite us in the
behind.

Best--
--Eric

________________________________

From: sbml-discuss-bounces@caltech.edu
[mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of Blinov,Michael
Sent: Wednesday, September 09, 2009 8:34 PM
To: SBML Discussion List
Subject: RE: [sbml-discuss] Proposed addition to L3 core


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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