Improving the Portability and Performance of jViz.RNA – A Dynamic RNA Visualization Software
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/ .
KeywordsRepulsion Force Large Sequence Java Virtual Machine Virtual Body Brute Force Algorithm
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