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

[Harold G. <Har...@gm...>]

Hi Lucian,

I have asked the CBO developers about the possibility of expanding the
ontology should we need to, and they are very willing to work with us on
this.

Also, CBO does have generic terms for "Creation" and "Deletion" of an
object -you can find them under the CBOProcess:FundamentalPhysicalProcess
branch. This means that though the current specification focuses on cell
behavior use cases as Chris mentioned, this formulation is still able to
embody the general behavior that was envisioned for the package.

Best,


On Thu, Oct 9, 2014 at 11:00 PM, Lucian Smith <luc...@gm...>
wrote:

> 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
>>>
>>>
>>>
>>>
>>>
>>>
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-- 
Harold Gómez
Bioinformatics PhD. Candidate, Boston University
Graduate School of Arts & Sciences