From: Lucian S. <luc...@gm...> - 2014-10-09 21:00:38
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Well, the point is that there *aren't* generic CBO terms for 'create' nor 'destroy'. Do we forsee that happening? I would have imagined that being very unlikely. -Lucian On Thu, Oct 9, 2014 at 1:55 PM, Chris J. Myers <my...@ec...> wrote: > Actually, it is possible to still do creation and destruction of arbitrary > SBML elements in the current draft, though we may need a new CBO term. To > perform cell division, one creates an event, tags it with the CBO term for > cell division, and adds a list of dynElements that includes all SBML > elements that must be duplicated during the cell division. Similarly, to > perform cell death, one creates an event, tags it with the CBO term for > cell death, and adds a list of dynElements that includes all SBML elements > that must be removed by cell death. > > If there are CBO terms for say "create" and "destroy", then the same > approach just described could be used to duplicate or remove any SBML > element but putting just that element in the list of dynElements. > > Indeed, though there is the question is whether or not this is ever a > useful thing to do. I think it might be, for example, if you want to > create say new types of species dynamically (perhaps existing species but > in a new state). I could also imagine as an efficiency, you might remove a > part of the model which can no longer contribute to the behavior. Anyway, > the point is that nothing has been lost in the formulation we have, but we > just have focussed on cell behavior use cases which don't perhaps exploit > the general behavior. > > Chris > > On Oct 9, 2014, at 2:45 PM, Lucian Smith <luc...@gm...> > wrote: > > 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 >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? 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