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


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  • From: jonovik at gmail.com (Jon Olav Vik)
  • Subject: [cellml-discussion] Auto-generate HDF5 from CellML?
  • Date: Mon, 10 Nov 2008 12:50:13 +0000 (UTC)
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




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