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[cellml-discussion] Auto-generate HDF5 from CellML?


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  • From: alan.garny at dpag.ox.ac.uk (Alan Garny)
  • Subject: [cellml-discussion] Auto-generate HDF5 from CellML?
  • Date: Fri, 14 Nov 2008 10:29:06 -0000
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of David Nickerson
> On Wed, Nov 12, 2008 at 9:38 PM, Jon Olav Vik <jonovik at gmail.com> wrote:
> > David Nickerson <david.nickerson at ...> writes:
> >> As for generic generation of HDF5 data structures from CellML models,
> >> I think this would need some thinking :) Is there a generic way to
> >> define a useful HDF5 data structure for any given CellML model? I'm
> >> not sure...
> >
> > To my layman's eyes it seems most CellML models are sets of coupled
> ordinary
> > differential equations, for which it should suffice to save state
> variables for
> > each time point, a model identifier and parameter values. (Parameter
> values must
> > be easily searchable, allowing retrieval of results for a given
> parameter set.)
> > Adding results from post-processing should be left to the end user.
>
> I think the searching should be performed with the CellML models
> rather than the HDF5 data files. The CellML models containing the
> various parametrizations of full models will contain a lot more useful
> data to query. You can then search your model archive for simulation
> descriptions (model instantiations) that meet certain criteria and can
> then retrieve the corresponding simulation data from the HDF5 data
> file. I'm currently not in favour of duplicating parameter values in
> the HDF5 data groups...but not sure about this yet :)

Duplication of information in any form or shape should be prohibited in my
view. That's a recipe for disaster at some point down the line.

Alan



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