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

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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
TOOL, DATABASES, IDENTIFICATIONS, PARSE

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Chicago
Barsnes, Harald, Marc Vaudel, Niklaas Colaert, Kenny Helsens, Albert Sickmann, Frode S Berven, and Lennart Martens. 2011. “Compomics-utilities: An Open-source Java Library for Computational Proteomics.” Bmc Bioinformatics 12.
APA
Barsnes, H., Vaudel, M., Colaert, N., Helsens, K., Sickmann, A., Berven, F. S., & Martens, L. (2011). compomics-utilities: an open-source Java library for computational proteomics. BMC BIOINFORMATICS, 12.
Vancouver
1.
Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, et al. compomics-utilities: an open-source Java library for computational proteomics. BMC BIOINFORMATICS. 2011;12.
MLA
Barsnes, Harald, Marc Vaudel, Niklaas Colaert, et al. “Compomics-utilities: An Open-source Java Library for Computational Proteomics.” BMC BIOINFORMATICS 12 (2011): n. pag. Print.
@article{1208280,
  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.},
  articleno    = {70},
  author       = {Barsnes, Harald and Vaudel, Marc and Colaert, Niklaas and Helsens, Kenny and Sickmann, Albert and Berven, Frode S and Martens, Lennart},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keyword      = {TOOL,DATABASES,IDENTIFICATIONS,PARSE},
  language     = {eng},
  pages        = {5},
  title        = {compomics-utilities: an open-source Java library for computational proteomics},
  url          = {http://dx.doi.org/10.1186/1471-2105-12-70},
  volume       = {12},
  year         = {2011},
}

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