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Development of a virtualized supercomputing environment for genomic analysis

Citation

Um, J-H and Choi, H and Song, S-K and Choi, S-P and Yoon, HM and Jung, H and Kim, T-H, Development of a virtualized supercomputing environment for genomic analysis, Journal of Supercomputing, 65, (1) pp. 71-85. ISSN 0920-8542 (2013) [Refereed Article]

Copyright Statement

Copyright 2012 Springer Science+Business Media, LLC

DOI: doi:10.1007/s11227-012-0752-3

Abstract

Recently the importance of genomic data analysis has been growing; one realizes necessity of the personalized treatment of human cancers. Next generation sequencing (NGS) technique is a cost-effective way to obtain such data sets for cancer data analysis. Hence, most of bioinformatics research groups use the NGS technique to obtain such data sets. The amount of NGS data is huge and rapidly growing; therefore, it requires supercomputing systems to be handled within a reasonable time. Bioinformatics researchers analyze the sets by using NGS applications such as BWA and BowTie, but those legacy applications have limited scalability and resource utilization on supercomputing systems.

To resolve this situation, we developed a virtualized technique by improving the resource utilization and scalability of NGS applications. First, to improve resource utilization, the virtualized system architecture is built by allocating virtual machines considering the limitation of resource utilization. Second, the virtualized system architecture considering data locality is presented to improve scalability. Finally, experimental results show that our virtualized system achieved approximately 30 % better performance than native systems. In addition, the performance of the system considering data locality achieves a speedup twice that of a system using a single-storage server.

Item Details

Item Type:Refereed Article
Keywords:supercomputing, virtualization, virtual cluster management, genomic analysis, NGS applications, MapReduce
Research Division:Information and Computing Sciences
Research Group:Computer Software
Research Field:Software Engineering
Objective Division:Information and Communication Services
Objective Group:Computer Software and Services
Objective Field:Computer Software and Services not elsewhere classified
Author:Kim, T-H (Dr Tai Kim)
ID Code:89251
Year Published:2013
Web of Science® Times Cited:2
Deposited By:Computing and Information Systems
Deposited On:2014-02-27
Last Modified:2017-11-13
Downloads:0

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