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[cellml-discussion] HDF5 licensing


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] HDF5 licensing
  • Date: Tue, 11 Nov 2008 12:57:26 +1300
My apologies - I should have looked a bit harder!

Randy Heiland wrote:
> The claim below surprised me (since I used to know and work with many
> of the HDF group), so I had a look at the license for HDF5:
>
> All rights reserved.
>
> Contributors: National Center for Supercomputing Applications (NCSA)
> at the University of Illinois, Fortner Software, Unidata Program
> Center (netCDF), The Independent JPEG Group (JPEG), Jean-loup Gailly
> and Mark Adler (gzip), and Digital Equipment Corporation (DEC).
>
> Redistribution and use in source and binary forms, with or without
> modification, are permitted for any purpose (including commercial
> purposes) provided that the following conditions are met:
>
> 1. Redistributions of source code must retain the above copyright
> notice, this list of conditions, and the following disclaimer.
> 2. Redistributions in binary form must reproduce the above
> copyright notice, this list of conditions, and the following
> disclaimer in the documentation and/or materials provided with the
> distribution.
> 3. In addition, redistributions of modified forms of the source or
> binary code must carry prominent notices stating that the original
> code was changed and the date of the change.
> 4. All publications or advertising materials mentioning features or
> use of this software are asked, but not required, to acknowledge that
> it was developed by The HDF Group and by the National Center for
> Supercomputing Applications at the University of Illinois at
> Urbana-Champaign and credit the contributors.
> 5. Neither the name of The HDF Group, the name of the University,
> nor the name of any Contributor may be used to endorse or promote
> products derived from this software without specific prior written
> permission from THG, the University, or the Contributor, respectively.
> -------------------------------
>
> I consider this about as close to open source as it gets and isn't
> much different that the CellML terms of use: http://www.cellml.org/terms
>
> -Randy
>
>
> On Nov 10, 2008, at 6:00 PM, cellml-discussion-request at cellml.org wrote:
>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 11 Nov 2008 11:42:28 +1300
>> From: James Lawson <j.lawson at auckland.ac.nz>
>> Subject: Re: [cellml-discussion] Auto-generate HDF5 from CellML?
>> To: CellML Discussion List <cellml-discussion at cellml.org>
>> Message-ID: <4918B8D4.5060403 at auckland.ac.nz>
>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>
>> 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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>>
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>>
>> End of cellml-discussion Digest, Vol 52, Issue 5
>> ************************************************
>
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