compomics-utilities: an open-source Java library for computational proteomics
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/12/70 |
| _version_ | 1828469806826782720 |
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| author | Helsens Kenny Colaert Niklaas Vaudel Marc Barsnes Harald Sickmann Albert Berven Frode S Martens Lennart |
| author_facet | Helsens Kenny Colaert Niklaas Vaudel Marc Barsnes Harald Sickmann Albert Berven Frode S Martens Lennart |
| author_sort | Helsens Kenny |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-11T04:44:19Z |
| format | Article |
| id | doaj.art-44584b79e6954a978a2d0c71942ebed6 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T04:44:19Z |
| publishDate | 2011-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-44584b79e6954a978a2d0c71942ebed62022-12-22T01:20:33ZengBMCBMC Bioinformatics1471-21052011-03-011217010.1186/1471-2105-12-70compomics-utilities: an open-source Java library for computational proteomicsHelsens KennyColaert NiklaasVaudel MarcBarsnes HaraldSickmann AlbertBerven Frode SMartens Lennart<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/12/70 |
| spellingShingle | Helsens Kenny Colaert Niklaas Vaudel Marc Barsnes Harald Sickmann Albert Berven Frode S Martens Lennart compomics-utilities: an open-source Java library for computational proteomics BMC Bioinformatics |
| title | compomics-utilities: an open-source Java library for computational proteomics |
| title_full | compomics-utilities: an open-source Java library for computational proteomics |
| title_fullStr | compomics-utilities: an open-source Java library for computational proteomics |
| title_full_unstemmed | compomics-utilities: an open-source Java library for computational proteomics |
| title_short | compomics-utilities: an open-source Java library for computational proteomics |
| title_sort | compomics utilities an open source java library for computational proteomics |
| url | http://www.biomedcentral.com/1471-2105/12/70 |
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