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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 106–117Cite as

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An Open Framework for Extensible Multi-stage Bioinformatics Software

An Open Framework for Extensible Multi-stage Bioinformatics Software

  • Gabriel Keeble-Gagnère23,
  • Johan Nyström-Persson24,
  • Matthew I. Bellgard23 &
  • …
  • Kenji Mizuguchi24 
  • Conference paper
  • 1612 Accesses

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

In research labs, there is often a need to customise software at every step in a given bioinformatics workflow, but traditionally it has been difficult to obtain both a high degree of customisability and good performance. Performance-sensitive tools are often highly monolithic, which can make research difficult. We present a novel set of software development principles and a bioinformatics framework, Friedrich, which is currently in early development. Friedrich applications support both early stage experimentation and late stage batch processing, since they simultaneously allow for good performance and a high degree of flexibility and customisability. These benefits are obtained in large part by basing Friedrich on the multiparadigm programming language Scala. We present a case study in the form of a basic genome assembler and its extension with new functionality. Our architecture has the potential to greatly increase the overall productivity of software developers and researchers in bioinformatics.

Keywords

  • Open Framework
  • Scala Code
  • Bioinformatics Application
  • Short Read Data
  • Early Stage Experimentation

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Author information

Authors and Affiliations

  1. Centre for Comparative Genomics, Murdoch University, Australia

    Gabriel Keeble-Gagnère & Matthew I. Bellgard

  2. National Institute of Biomedical Innovation, Japan

    Johan Nyström-Persson & Kenji Mizuguchi

Authors
  1. Gabriel Keeble-Gagnère
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  2. Johan Nyström-Persson
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  3. Matthew I. Bellgard
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  4. Kenji Mizuguchi
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Cite this paper

Keeble-Gagnère, G., Nyström-Persson, J., Bellgard, M.I., Mizuguchi, K. (2012). An Open Framework for Extensible Multi-stage Bioinformatics Software. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_10

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_10

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  • Print ISBN: 978-3-642-34122-9

  • Online ISBN: 978-3-642-34123-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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