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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 82–93Cite as

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Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization Software

Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization Software

  • Boris Shabash23,
  • Kay Wiese23 &
  • Edward Glen23 
  • Conference paper
  • 1575 Accesses

  • 1 Citations

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

Abstract

In this paper, four methods were explored for improving the performance of jViz.RNA’s structure drawing algorithm when dealing with large sequences; First, the approximation based Barnes-Hut algorithm was explored. Second, the effects of using multithreading were measured. additionally, dynamic C libraries, which integrate C code into the JavaTM environment, were investigated. Finally, a technique termed structure recall was examined.

The results demonstrated that the use of the Barnes-Hut algorithm produced the most drastic improvements in run-time, but distorts the structure if too crude of an approximation is used. Multithreading and integration of C code proved to be favorable approaches since these improved the speed at which calculations are done, without distorting the structures.

jViz.RNA is available to download from http://jviz.cs.sfu.ca/ .

Keywords

  • Repulsion Force
  • Large Sequence
  • Java Virtual Machine
  • Virtual Body
  • Brute Force Algorithm

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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References

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Author information

Authors and Affiliations

  1. School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada

    Boris Shabash, Kay Wiese & Edward Glen

Authors
  1. Boris Shabash
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  2. Kay Wiese
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  3. Edward Glen
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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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Shabash, B., Wiese, K., Glen, E. (2012). Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization 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_8

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  • DOI: https://doi.org/10.1007/978-3-642-34123-6_8

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  • Print ISBN: 978-3-642-34122-9

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