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Re: [h5md-user] H5MD for proteins

From: Olaf Lenz
Subject: Re: [h5md-user] H5MD for proteins
Date: Tue, 10 Sep 2013 15:14:33 +0200
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On 09/10/2013 12:21 PM, Konrad Hinsen wrote:
> I am not sure I want my 10 GB HDF5 trajectories to pass through an 
> XML phase during construction.

Indeed, but I didn't say that you *have* to go via XML. You just would
have the option to use it, and that would be a great help.

> Yes, that's a good point of view. Something else we can do is provide
> a validation program for H5MD data.

I had thought that the HDF5 DTD might provide that

Unfortunately, it just seems to provide a DTD that describes the
possible output of "hdf5dump -x".

Maybe we can use "hdf5dump -x" in conjunction with an XML validator to
validate H5MD-files?

> BTW, I chose the same approach for Mosaic. In HDF5, every Mosaic data
> item has a "type stamp" (an attribute) that identifies it with its
> Mosaic type and the Mosaic version number. The Mosaic library can
> validate such data items for conformance.

I will have a look at Mosaic, but didn't find the time so far. It
definitely looks interesting.

> Me too :-) It's obviously useful for structuring (and sharing) 
> programs that work on trajectory data. What I question is the 
> scientific utility because the semantic information about the data in
> the file is so weak. It's not that there is no semantic information,
> but even 90% of the semantic information you need is 10% short of
> something usable.

I propose to add semantic information step-by-step via modules. Like
this we can maybe avoid to render the format unusable for some
applications. That is why I would also vote to keep the base module as
simple as possible.


Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607

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