tzaeschke / compomics-utilities

Open source Java library for computational proteomics

compomics-utilities

• What is compomics-utilities?

• Projects Using compomics-utilities

• Using compomics-utilities

• Download

• Maven Dependency

• Screenshots

• Bioinformatics for Proteomics Tutorial

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compomics-utilities publication:

• 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.

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What is compomics-utilities?

The Computational Omics and Systems Biology Group 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	interpretation of proteomics identification results	Vaudel et al: Nature Biotechnol. 2015 Jan;33(1):22–24.
MetaProteomeAnalyzer	analyzing meta-proteomics data	Muth et al: J Proteome Res. 2015 (in press).
DeNovoGUI	de novo sequencing of tandem mass spectra	Muth at al: J Proteome Res. 2014 Feb 7;13(2):1143-6.
pride-asap	uniform annotation of identified spectra stored in PRIDE	Hulstaert et al: J Proteomics. 2013 Apr 17
ProteoCloud	proteomics cloud computing pipeline	Muth et al: J Proteomics. 2013 Aug 2;88:104-8
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	Barsnes et al: J Proteome Res. 2018 (in press) 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. Also check the JavaDoc.

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Download

We strongly recommend Maven when using compomics-utilities, as this makes sure that one gets all the dependencies right. See Maven Dependency below.

All compomics-utilities builds are available here.

See also the JavaDoc.

If you for some reason cannot use Maven and need a complete build of compomics-utilities, please let us know and we will send you the latest build as a zip file.

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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>

<repositories>

    <!-- Compomics Genesis Maven 2 repository -->
    <repository>
        <id>genesis-maven2-repository</id>
        <name>Genesis maven2 repository</name>
        <url>http://genesis.UGent.be/maven2</url>
        <layout>default</layout>
    </repository>

    <!-- old EBI repository -->
    <repository>
        <id>ebi-repo</id> 
        <name>The EBI internal repository</name>
        <url>http://www.ebi.ac.uk/~maven/m2repo</url>
    </repository>

    <!-- EBI repository -->
    <repository>
        <id>pst-release</id>
        <name>EBI Nexus Repository</name>
        <url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
    </repository>
    
</repositories>

Update the version number to latest released version, see the Maven repository.

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Screenshots

(Click on figure to see the full size version)

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