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


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  • From: david.nickerson at gmail.com (David Nickerson)
  • Subject: [cellml-discussion] Auto-generate HDF5 from CellML?
  • Date: Fri, 14 Nov 2008 14:12:53 +0800
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 :)

> Actually, I think writing a HDF5 structure generator could be almost like
> just
> adding another output format to the code generator.

pretty similar, I think. Certainly something that would be based on
the current code generation service...

>> Do you imagine a tool which for a given CellML model (or perhaps more
>> realistically for a given chunk of CellML simulation metadata) will
>> produce essentially a template HDF5 data group with standardized
>> structure. Then your simulation tool would grab that data group and
>> populate the simulation results.
>
> Yes!

I have added this feature request/suggestion to the tracker
(https://tracker.physiomeproject.org/show_bug.cgi?id=1492) to better
enable tracking further developments along these lines. Anyone
interested in implementing or using such a feature, or simply
observing the developments, should add themselves to the CC list for
the tracker item.

>> Or would some kind of simulation data storage and retrieval service
>> sitting on top of the CellML API be more what you are after? Then I
>> guess that would allow for different underlying persistent data stores
>> to be utilised...
>
> Yes, though I personally don't feel the need for this at the moment.

agreed, although possibly the above could be used as a template to
help with a development like this...


Andre.


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