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 2012 Springer Science+Business Media, LLC
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 Type:||Refereed Article|
|Keywords:||supercomputing, virtualization, virtual cluster management, genomic analysis, NGS applications, MapReduce|
|Research Division:||Information and Computing Sciences|
|Research Group:||Software engineering|
|Research Field:||Software testing, verification and validation|
|Objective Division:||Information and Communication Services|
|Objective Group:||Information systems, technologies and services|
|Objective Field:||Information systems, technologies and services not elsewhere classified|
|UTAS Author:||Kim, T-H (Dr Tai Kim)|
|Web of Science® Times Cited:||2|
|Deposited By:||Information and Communication Technology|
Repository Staff Only: item control page