compomics-utilities

What is compomics-utilities?
Projects Using compomics-utilities
Using compomics-utilities
Download
Updates
Maven Dependency
Screenshots

compomics-utilities Publications:

Barsnes et al: BMC Bioinformatics. 2011 Mar 8;12(1):70.
If you use compomics-utilities as part of a paper, please include the reference above.

What is compomics-utilities?

The Computational Omics and Systems Biology Group at the University of Ghent develops various bioinformatics tools for analyzing omics data.

compomics-utilities is a library containing code shared by many of our research projects, amongst others containing panels for visualizing spectra and chromatograms and objects for representing peptides and proteins etc. We believe that this library can be of use to other research groups doing computational proteomics, and have therefore made it available as open source.

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Projects using compomics-utilities

Project	Description	Publication
PeptideShaker	visualization of proteomics identifications from multiple search engines	(in preparation)
thermo-msf-parser	parser and viewer for thermo msf files	Colaert et al: J Proteome Res. 2011;10(8):3840-3
SearchGUI	graphical user interface for proteomics identification search engines	Vaudel et al: Proteomics 2011;11(5):996-9
XTandem Parser	java parser for X!Tandem output xml files	Muth et al: Proteomics 2010;10(7):1522-4
jmzML	java implementation of the PSI-MS mzML specification	Côté et al: Proteomics 2010;10(7):1332-5
Fragmentation Analyzer	analyzing MS/MS fragmentation data	Barsnes et al: Proteomics 2010;10(5):1087-90
ms_lims	mass spectrometry based proteomics information management system	Helsens et al: Proteomics 2010;10(6):1261-4
Rover	visualize and validate quantitative proteomics data	Colaert et al: Proteomics 2010;10(6):1226-9
IceLogo	next-generation visualization of protein consensus sequences	Colaert et al: Nature Methods 2009;6(11):786-7
OMSSA Parser	java parser for OMSSA omx files	Barsnes et al: Proteomics 2009;9(14):3772-4
Peptizer	automating manual validation of MS/MS search results	Helsens et al: MCP 2008;7(12):2363-72
MascotDatfile	java API for MS/MS search results by Mascot	Helsens et al: Proteomics 2007;7(3):364-6
DBToolkit	manipulating fasta sequence databases	Martens et al: Bioinformatics 2005;21(17):3584-5

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Using compomics-utilities

For example code and demos showing how the compomics-utilities library can be used in your project see Examples.

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Download

The zip file in the downloads section contains the compomics-utilities jar file and all the libraries needed to run or build the tool.

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Updates

See Changes for the latest changes.

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Maven dependency

compomics-utilities is available for use in Maven projects:

<dependency>
    <groupId>com.compomics</groupId>
    <artifactId>utilities</artifactId>
    <version>X.Y.Z</version>
</dependency>

<repository>
    <id>genesis-maven2-repository</id>
    <name>Genesis maven2 repository</name>
    <url>http://genesis.UGent.be/maven2</url>
</repository>

Update the version number to latest released version.

Note that compomics-utilities does not yet build in Maven 3. We are working on fixing this but in the meantime please use Maven 2 to build compomics-utilities.

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Screenshots

(Click on figure to see the full size version)

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