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, [EMAIL PROTECTED] wrote:
------------------------------
Message: 2
Date: Tue, 11 Nov 2008 11:42:28 +1300
From: James Lawson <[EMAIL PROTECTED]>
Subject: Re: [cellml-discussion] Auto-generate HDF5 from CellML?
To: CellML Discussion List <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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
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