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Bioinformatics Advance Access published online on January 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk015
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 30, 2005
Revised December 5, 2005
Accepted December 15, 2005

Applications note

ProteomeCommons.org JAF: reference information and tools for proteomics

J. A. Falkner 1 *, J. W. Falkner 1, and P. C. Andrews 1

1 Dept. Biological Chemistry, University of Michigan, Ann Arbor MI, 48104

* To whom correspondence should be addressed.
J. A. Falkner, E-mail: jfalkner{at}umich.edu


  Abstract

Summary: Analysis of proteomics data, specifically mass spectrometry data, commonly relies on libraries of known information such as atomic masses, known stable isotopes, atomic compositions of amino acids, observed modifications of known amino acids, and ion masses that directly correspond to known amino acid sequences. The Java Analysis Framework (JAF) for proteomics provides a freely usable, open-source library of Java code that abstracts all of the aforementioned data, enabling more rapid development of proteomics tools. The JAF also includes several user tools that can be run directly from a web browser.

Availability: The current version and an archive of all older versions of the Java Analysis Framework for Proteomics is freely available, including complete source-code, at http://www.proteomecommons.org/current/511/.

Associate Editor: Jonathan Wren
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J. A. Falkner, J. W. Falkner, and P. C. Andrews
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
Bioinformatics, January 15, 2007; 23(2): 262 - 263.
[Abstract] [Full Text] [PDF]


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