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

Harald Barsnes, Marc Vaudel, Niklaas Colaert UGent, Kenny Helsens UGent, Albert Sickmann, Frode S Berven and Lennart Martens UGent (2011) BMC BIOINFORMATICS. 12.
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
TOOL, DATABASES, IDENTIFICATIONS, PARSE
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
12
article number
70
pages
5 pages
Web of Science type
Article
Web of Science id
000288534700002
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
2.751 (2011)
JCR rank
6/46 (2011)
JCR quartile
1 (2011)
ISSN
1471-2105
DOI
10.1186/1471-2105-12-70
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1208280
handle
http://hdl.handle.net/1854/LU-1208280
date created
2011-04-13 14:12:36
date last changed
2016-12-21 15:42:26
@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},
}

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.