Re: [Psidev-ms-dev] MSData: C++ library for mzML reading/writing

[Eric D. <ede...@sy...>]

Hi Darren, many thanks for writing this and making it available. As
Angel recently pointed out, we really need to demonstrate that mzML
works in an existing pipeline before we release. I would very much like
to get a working version of the RAMP library for mzML as this would
allow us to test our tools with mzML and close the loop. I hope your
very nice library here can help us implement this quickly.

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Thanks!

Eric

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________________________________

From: psi...@li...
[mailto:psi...@li...] On Behalf Of
Kessner, Darren E.
Sent: Monday, January 21, 2008 3:48 PM
To: psi...@li...
Subject: [Psidev-ms-dev] MSData: C++ library for mzML reading/writing

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Hi all,

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I just wanted to introduce a C++ library I've been working on for
handling mzML (among other things).

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Some background:  Our group (Spielberg Family Center for Applied
Proteomics, Cedars-Sinai Medical Center) has a number of software tools
for analyzing RAW and mzXML data files.  This library (MSData) is the
next version of our data file access layer.  The MSData library
implements a C++ representation of mzML.=20

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Current implemented functionality:

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 - compile-time parsing of the psi-ms.obo controlled vocabulary file to
generate C++ code

   for typesafe use of the controlled vocabulary terms

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 - mzML <-> MSData data structure mapping, including reading/writing
mzML XML fragments from/to

   C++ iostreams

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 - diff functionality for each MSData data structure

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 - binary data array encoding with 64-32 bit conversions and
endianization=20

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 - abstract interface to spectrum binary data, to allow lazy evaluation
of binary data

   backed by data files

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Next steps:

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 - mzXML reading/writing, RAW reading

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 - simple analysis interface for accessing scan data and common
meta-data fields

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I put a source package here:

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http://www.sfcap.cshs.org/private

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login: psidev

pass: pwiz

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We will be making this library available open source, as soon as we
finish wading through our legal department's bureaucracy.

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Please have a look, and feel free to email me with any questions,
comments, or suggestions!

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Darren

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Darren Kessner

Scientific Programmer

Dar...@cs...

310-423-9538

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Spielberg Family Center for Applied Proteomics

Cedars-Sinai Medical Center

http://www.sfcap.cshs.org/

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