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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: Tue, 11 Nov 2008 09:06:19 +0800
> Sounds really interesting - the one reservation I'd have, however, is that
> HDF5 doesn't appear to be open-source.

just to note that HDF5 is open source. License available here:
ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/COPYING


Andre.


>
> 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
>>
>>
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>>
>
>
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