Paper Info
Title
Improving the portability and performance of jViz.RNA --- a dynamic RNA visualization software
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/ .
Year
DOI
Venue
2012
10.1007/978-3-642-34123-6_8
PRIB
Keywords
Field
DocType
dynamic rna visualization software,large sequence,barnes-hut algorithm,drastic improvement,structure recall,c code,favorable approach,javatm environment,dynamic c library
Multithreading,Brute-force search,Computer science,Parallel computing,Software portability,Artificial intelligence,Bioinformatics,Software visualization,Machine learning,Java virtual machine
Conference
Volume
ISSN
Citations 
7632
0302-9743
2
PageRank 
References 
Authors
0.37
7
3
Name
Order
Citations
PageRank
Boris Shabash172.22
Kay Wiese240.83
Edward Glen3454.20