Re: [Psidev-ms-dev] Separate binary file for very large data sets?

[Brian P. <bri...@in...>]

I wonder if it wouldn't make as much sense to treat the mzData file as =
the
"binary file" and come up with a sort of summary schema of your own that
could point into the mzData file.  You'd get maximum reuse of community
source code that way.

But first, I'd say try it with straight-up mzData with compressed peak =
lists
and see if you really need to go to the bother of a separate file.  I'm
guessing you'll be pleasantly surprised.  Plus, I really, really dislike =
the
use of interdependent files - one or the other is forever getting out of
synch, lost, renamed, etc.

Hope this helps,

Brian Pratt
www.insilicos.com

-----Original Message-----
From: psi...@li...
[mailto:psi...@li...] On Behalf Of =
Andreas
R=F6mpp
Sent: Friday, April 20, 2007 8:45 AM
To: psi...@li...;
And...@an...
Subject: [Psidev-ms-dev] Separate binary file for very large data sets?

Hello everybody,

We develop software for imaging mass spectrometry in the framework of a
project funded by the European Union. We intend to use dataXML as a =
standard
format to exchange data between the different partner labs and also (as =
far
as possible) as the internal data format for a joint processing software
suite. However, we run into the problem of very large data sets which =
can
easily exceed 1GB (e.g. 256
*256 pixels with one high resolution mass spectrum each). Therefore we
thought about storing the spectrum data ('MassToChargeRatioArray' and '=20
'IntensityArray') in a separate binary file. This would make data =
handling
much faster and easier (e.g. when parsing the XML file). So instead of
writing the binary data in the XML file we plan to include a link to a
separate file (file location, start and end position of spectrum in =
binary
file).
This problem is somewhat similar to the already discussed issue of an =
index
file.
Would it be possible to include such an option (external binary file) =
into
the dataXML standard?

Best regards,
Andreas

--
-------------------------------------------------------------------------=
---
-------------
Dr. Andreas Roempp
Institute of Inorganic and Analytical Chemistry
- Analytical Chemistry -
Justus Liebig University Giessen
Schubertstrasse 60, Build. 16
D-35392 Giessen
Germany

phone:  +49-641-99 34802
fax:    +49-641-99 34809
email: And...@an...
Internet: http://www.uni-giessen.de/analytik/




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