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Managing expectations when publishing tools and methods for computational proteomics

(2015) JOURNAL OF PROTEOME RESEARCH. 14(5). p.2002-2004
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is Often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool Can be considered mature, and-by that time it might be difficult for a new publication to be accepted, because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a Way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the implementation is not necessarily production-ready. Research Articles present both a novel idea and mature implementation that has been suitably benchmarked. Application Notes focus on a mature and tested tool or concept and need not be novel but should offer advancement from improved,quality, ease of use, and/or implementation. Organizing computational proteomics contributions into these three manuscript types will facilitate the review process and will also enable readers to identify the maturity and applicability of the tool for their own workflows.
Keywords
manuscript types, bioinformatics, computational mass spectrometry

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Citation

Please use this url to cite or link to this publication:

Chicago
Martens, Lennart, Oliver Kohlbacher, and Susan T Weintraub. 2015. “Managing Expectations When Publishing Tools and Methods for Computational Proteomics.” Journal of Proteome Research.
APA
Martens, Lennart, Kohlbacher, O., & Weintraub, S. T. (2015). Managing expectations when publishing tools and methods for computational proteomics. JOURNAL OF PROTEOME RESEARCH.
Vancouver
1.
Martens L, Kohlbacher O, Weintraub ST. Managing expectations when publishing tools and methods for computational proteomics. JOURNAL OF PROTEOME RESEARCH. 2015. p. 2002–4.
MLA
Martens, Lennart, Oliver Kohlbacher, and Susan T Weintraub. “Managing Expectations When Publishing Tools and Methods for Computational Proteomics.” JOURNAL OF PROTEOME RESEARCH 2015 : 2002–2004. Print.
@misc{6895241,
  abstract     = {Computational tools are pivotal in proteomics because they are crucial for identification, quantification, and statistical assessment of data. The gateway to finding the best choice of a tool or approach for a particular problem is frequently journal articles, yet there is Often an overwhelming variety of options that makes it hard to decide on the best solution. This is particularly difficult for nonexperts in bioinformatics. The maturity, reliability, and performance of tools can vary widely because publications may appear at different stages of development. A novel idea might merit early publication despite only offering proof-of-principle, while it may take years before a tool Can be considered mature, and-by that time it might be difficult for a new publication to be accepted, because of a perceived lack of novelty. After discussions with members of the computational mass spectrometry community, we describe here proposed recommendations for organization of informatics manuscripts as a Way to set the expectations of readers (and reviewers) through three different manuscript types that are based on existing journal designations. Brief Communications are short reports describing novel computational approaches where the implementation is not necessarily production-ready. Research Articles present both a novel idea and mature implementation that has been suitably benchmarked. Application Notes focus on a mature and tested tool or concept and need not be novel but should offer advancement from improved,quality, ease of use, and/or implementation. Organizing computational proteomics contributions into these three manuscript types will facilitate the review process and will also enable readers to identify the maturity and applicability of the tool for their own workflows.},
  author       = {Martens, Lennart and Kohlbacher, Oliver and Weintraub, Susan T},
  issn         = {1535-3893},
  keyword      = {manuscript types,bioinformatics,computational mass spectrometry},
  language     = {eng},
  number       = {5},
  pages        = {2002--2004},
  series       = {JOURNAL OF PROTEOME RESEARCH},
  title        = {Managing expectations when publishing tools and methods for computational proteomics},
  url          = {http://dx.doi.org/10.1021/pr501318d},
  volume       = {14},
  year         = {2015},
}

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