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

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dc.contributor.author Barsnes, Harald
dc.contributor.author Vaudel, Marc
dc.contributor.author Colaert, Niklaas
dc.contributor.author Helsens, Kenny
dc.contributor.author Sickmann, Albert
dc.contributor.author Berven, Frode S.
dc.contributor.author Martens, Lennart
dc.date.accessioned 2011-04-07T08:15:03Z
dc.date.available 2011-04-07T08:15:03Z
dc.date.issued 2011-03-08
dc.identifier.citation BMC Bioinformatics 12:70 en_US
dc.identifier.issn 1471-2105
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-12-70
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 en_US
dc.publisher BioMed Central en
dc.rights Copyright 2011 Barsnes et al; licensee BioMed Central Ltd. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title Compomics-utilities: an open-source Java library for computational proteomics en_US
dc.type Peer reviewed en
dc.type Journal article en
dc.rightsHolder Barsnes et al. en_US
dc.type.version publishedVersion en_US
bora.cristinID 830770


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Copyright 2011 Barsnes et al; licensee BioMed Central Ltd. Except where otherwise noted, this item's license is described as Copyright 2011 Barsnes et al; licensee BioMed Central Ltd.

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