Abstract
OBIGrid provides high-throughput GRIDBLAST services (OBIGbs) for researchers who need to deal with many BLAST query sequences at one time by exploiting both distributed processing and parallel processing. A new application-oriented grid framework has been introduced to split a BLAST query into independent sub-queries and to execute the sub-queries on remote personal computers and PC clusters connected by a virtual private network (VPN) over the Internet. The framework consists of five functional units: query splitter, job dispatcher, task manager, result collector and result formatter. They enable us to develop a cooperative GRIDBLAST system between a server and heterogeneous remote worker nodes: which consist of various computer architectures, different BLAST implementations and different Job schedulers operated by local resource management policy. The OBIGbs can execute 29,941 PSI-BLAST query sequences in 8.31 hours when using 230 CPUs in total and can return a 1.37 Giga byte result file.
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References
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)
Konagaya, A., Konishi, F., Hatakeyama, M.: The Superstructure Toward Open Bioinformatics Grid. New Generation Computiong 22(2) (2004) (in printing)
Satou, K., Nakashima, Y., Tsuji, S., Defago, X., Konagaya, A.: An Integrated System for Distributed Bioinformatics Environment on Grids. In: Konagaya, A., Satou, K. (eds.) LSGRID 2004. LNCS (LNBI), vol. 3370, pp. 8–19. Springer, Heidelberg (2005)
von Laszewski, G., Foster, I., Gawor, J., Lane, P.: A Java Commodity Grid Kit. Concurrency and Computation: Practice and Experience 13(8-9), 643–662 (2001)
Foster, I., Kesselman, C., Nick, J., Tuecke, S.: The Physiology of the Grid: An Open Grid Services Architecture for Distributed Systems Integration. In: Open Grid Service Infrastructure WG, Global Grid Forum, June 22 (2002)
Ishikawa, Y., Tezuka, H., Hori, A., Sumimoto, S., Takahashi, T., O’Carroll, F., Harada, H.: RWC PC Cluster II and SCore Cluster System Software — High Performance Linux Cluster. In: Proceedings of the 5th Annual Linux Expo, pp. 55–62 (1999)
Basney, J., Livny, M.: Deploying a High Throughput Computing Cluster. In: Buyya, R. (ed.) High Performance Cluster Computing, ch. 5, May 1999, vol. 1. Prentice Hall PTR, Englewood Cliffs (1999)
The RIKEN Genome Explotion Research Group Phase II Team and the FANTOM Consortium. Functional annotation of a full-length mouse cDNA collection, Nature 409, 685–690 (2001)
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Konishi, F., Konagaya, A. (2005). The Architectural Design of High-Throughput BLAST Services on OBIGrid. In: Konagaya, A., Satou, K. (eds) Grid Computing in Life Science. LSGRID 2004. Lecture Notes in Computer Science(), vol 3370. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32251-1_4
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DOI: https://doi.org/10.1007/978-3-540-32251-1_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25208-5
Online ISBN: 978-3-540-32251-1
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