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


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] Auto-generate HDF5 from CellML?
  • Date: Tue, 11 Nov 2008 11:42:28 +1300
Hi Jon Olav,

Sounds really interesting - the one reservation I'd have, however, is
that HDF5 doesn't appear to be open-source.

Cheers,
James

Jon Olav Vik wrote:
> Dear all,
>
> I'm considering HDF5 for my storage needs in simulating a CellML model
> under
> multiple parameter scenarios. HDF5 is designed for efficient storage,
> retrieval, navigation and subsetting of huge data sets [1], with annotation
> [2]. I plan on storing both raw and post-processed data, so that if I
> detect
> problems at a higher level, I can go back and look at details and possibly
> re-
> run those simulations. David Nickerson described a similar approach in an
> earlier post [3].
>
> However, setting up the data structure with annotations for physical units
> and
> such is quite time-consuming. On the other hand, the CellML representation
> holds all the required information. It would be very helpful to
> auto-generate
> an HDF5 data structure to hold output from simulations of CellML models.
>
> Such a tool should be fairly easy to write for someone familiar with both
> HDF5
> and CellML, and would apply to all possible CellML models. I guess it would
> be
> overly restrictive to make an output format part of the CellML metadata
> specification. However, offering a standard output format would save
> duplication of effort and make it easier to share simulation results for
> further visualization and analysis.
>
> I'd like the opinions of the CellML regulars, in particular whether
> anything
> similar has been discussed previously.
>
> Best regards,
> Jon Olav Vik
>
> [1] http://www.hdfgroup.org/about/hdf_technologies.html
> [2]
> http://www.hdfgroup.org/training/HDFtraining/UsersGuide/MF_Annot.fm1.html
> [3] http://article.gmane.org/gmane.text.xml.cellml.general/234/match=hdf5
>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>

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