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Compomics-utilities: an open-source Java library for computational proteomics

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dc.contributor.author Barsnes, Harald eng
dc.contributor.author Vaudel, Marc eng
dc.contributor.author Colaert, Niklaas eng
dc.contributor.author Helsens, Kenny eng
dc.contributor.author Sickmann, Albert eng
dc.contributor.author Berven, Frode S. eng
dc.contributor.author Martens, Lennart eng
dc.date.accessioned 2011-04-07T08:15:03Z
dc.date.available 2011-04-07T08:15:03Z
dc.date.issued 2011-03-08 eng
dc.identifier.citation BMC Bioinformatics 12:70 en_US
dc.identifier.issn 1471-2105 eng
dc.identifier.uri http://hdl.handle.net/1956/4629
dc.description.abstract Background The growing interest in the field of proteomics has increased the demand for software tools and applications that process and analyze the resulting data. And even though the purpose of these tools can vary significantly, they usually share a basic set of features, including the handling of protein and peptide sequences, the visualization of (and interaction with) spectra and chromatograms, and the parsing of results from various proteomics search engines. Developers typically spend considerable time and effort implementing these support structures, which detracts from working on the novel aspects of their tool. Results In order to simplify the development of proteomics tools, we have implemented an open-source support library for computational proteomics, called compomics-utilities. The library contains a broad set of features required for reading, parsing, and analyzing proteomics data. compomics-utilities is already used by a long list of existing software, ensuring library stability and continued support and development. Conclusions As a user-friendly, well-documented and open-source library, compomics-utilities greatly simplifies the implementation of the basic features needed in most proteomics tools. Implemented in 100% Java, compomics-utilities is fully portable across platforms and architectures. Our library thus allows the developers to focus on the novel aspects of their tools, rather than on the basic functions, which can contribute substantially to faster development, and better tools for proteomics. en_US
dc.language.iso eng eng
dc.publisher BioMed Central eng
dc.rights Attribution CC BY eng
dc.rights.uri http://creativecommons.org/licenses/by/2.0 eng
dc.title Compomics-utilities: an open-source Java library for computational proteomics eng
dc.type Peer reviewed eng
dc.type Journal article eng
dc.rights.holder Copyright 2011 Barsnes et al; licensee BioMed Central Ltd.
dc.rights.holder Barsnes et al. eng
dc.type.version publishedVersion eng
bora.peerreviewed Peer reviewed eng
bora.cristinID 830770 eng
bibo.doi http://dx.doi.org/10.1186/1471-2105-12-70 eng
dc.identifier.cristinID 830770 eng
dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-12-70


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