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

  • Boris Shabash
  • Kay Wiese
  • Edward Glen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7632)


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 .


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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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Boris Shabash
    • 1
  • Kay Wiese
    • 1
  • Edward Glen
    • 1
  1. 1.School of Computing ScienceSimon Fraser UniversityBurnabyCanada

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