Re: [sbml-dynamic] Draft Specification for Dynamic Structures Package

[Lucian S. <luc...@gm...>]

Hmm, I don't think that's *quite* true.  The original package's stated goal
was to enable the creation (and destruction) of SBML elements dynamically,
full stop.  Enabling the modeling of cellular processes was a prominent
use-case, but not the only potential use-case.

However, in its current form, the package has completely hitched itself to
the CBO, and in so doing, slightly reduced the scope of the original
package idea.  It has also expanded its scope to other cellular processes
besides creation and destruction, but it has still lost the ability to
define creation and destruction outside the scope of *cell* creation and
*cell* destruction.

Personally, I think the focus of the new scope lends itself better to its
use and uptake by the multicellular community, and believe that, overall,
it's a worthy direction for an SBML package, but it does raise the
question:  is there anyone out there who wants creation and destruction of
SBML elements outside of cell creation and destruction?  If not, great;
let's just rename the package and move on.  But if so, we'll need to
decide:  do we try to accommodate those people within this newly-scoped
package, or do we split off and leave that group the old 'dynamic' package,
and move forward with a newly-renamed package for CBO?

That's probably a question worthy of sbml-discuss, if not an actual poll.

-Lucian

On Thu, Oct 9, 2014 at 6:29 AM, Chris J. Myers <my...@ec...> wrote:

>
> >
> >> I really think the best way forward is to rebrand what we are doing
> >> as "multi-cellular" modeling.  While doing multi-cellular modeling
> >> can be done in a limited fashion in core, it does not really handle
> >> well what people in this field are doing.
> >
> > You mean, rename the dynamics package, or simply call this current work
> "the Multicellular Modeling package" and leave the "dynamics" package alone?
> >
> If I understand you, your question asks whether or not this package
> replaces the dynamics package or is really a new package.  It is a bit of
> both.  The original dynamics package goal was to enable the creation of
> SBML elements dynamically in order to enable the modeling of cellular
> processes.  The current version of the package still does this, though
> perhaps in a more specialized fashion, but it adds to it the use of CBO and
> coarse spatial concept for location.  My vote would be that this replaces
> the dynamics package, since it is basically a superset of the original
> goals.  A better name though is in order.  I think my current preference
> for name would be Cellular Dynamics Package.  It allows us to keep "dyn" as
> the shorthand.  It allows for the modeling of single cells or populations.
> It would not be confused with the Multistate Modeling Package.
>
> Chris
>
>
>
>
>
>
>
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