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

[James O. <jam...@cs...>]

Dear all

Sorry for coming late to this discussion. I am one of the Developers of
Chaste (http://www.cs.ox.ac.uk/chaste/) which as part of it contains a
multicellular modelling framework.
The framework allows you to model multiple interacting cells, selecting
from On and Off lattice modeling approaches (CA, Cell Potts, Cell Centre
and Cell Vertex Models). It also allows the specification of subcellular
behaviour (through cell cycle models) which couple to the cells.

The main thing i think that is important for this discussion is that in the
framework we keep track of the cells topology (and connectivity) in each
simulation type and this allows us to so the same operations on each
paradigm (for example solve PDEs or cell cell communication). This could be
a possible level that the language could specify events on.
It is the topology and connectivity of cells that is always updated on cell
division or death. However there are also occurrences where the topology
changes due to the movement of cells, maybe this should be captured
separately.

We have come at the problem from an implementation point of view rather
than ontologies or abstractions but are very keen to make things more
interchangeable.

Thanks

James



On Thu, Oct 9, 2014 at 2:29 PM, 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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-- 
Dr James Osborne

Senior Researcher, Computational Biology,
University of Oxford Department of Computer Science.
Web: http://www.cs.ox.ac.uk/people/james.osborne/
Tel: +44 (0)1865 610671

Visiting Scientist, Computational Science Laboratory,
Microsoft Research Limited