Abstract
In this paper, we present BioGrid, a novel computing resource that combines advantages of grid computing technology with bioinformatics parallel applications. The grid environment permits the sharing of a large amount of idle computing resources and data. The investigation of bioinformatics demands orders of magnitude of computing resources and in parallel, the biological data are growing in such a high speed. By using BioGrid, we plan to integrate and share resources and biological data using the grid computing technology. Still in this paper, the well-known FASTA application is performed as matter of testing and analysis in our grid computing platform, as goal to show the improved efficiency and reduced computation time.
This research is supported in part by the National Science Council, Taiwan, under grant NSC93-2213-E-126-010.
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References
Trelles, O.: On the Parallelization of Bioinformatics Applications. Briefings in Bioinformatics 2 (May 2001), Available from: http://www.ac.uma.es/~ots/papers/survey.pdf
Li, K.-B.: ClustalW-MPI: ClustalW Analysis Using Distributed and Parallel Computing. Bioinformatics 19(12), 1585–1586 (2003)
Hokamp, K., Shields, D.C., Wolfe, K.H., Caffrey, D.R.: Wrapping up BLAST and other applications for use on UNIX clusters. Bioinformatics 19(3), 441–442 (2003)
Schmidt, H.A., Strimmer, K., Vingron, M., von Haeseler, A.: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18(3), 502–504 (2002)
Karo, M., Dwan, C., Freeman, J., Weissman, J., Livny, M., Retzel, E.: Applying Grid Technologies to Bioinformatics. In: 10th IEEE International Symposium on High Performance Distributed Computing (HPDC-10 2001). IEEE Computer Society, Los Alamitos (2001)
Global Grid Forum, Available from: http://www.ggf.org
Foster, I., Kesselman, C.: The Grid: Blueprint for a New Computing Infrastructure. Morgan Kaufmann, San Francisco (1999)
Foster, I.: The Grid: A New Infrastructure for 21st Century Science. Physics Today 55(2), 42–47 (2002)
SETI@home: Search for Extraterrestrial Intelligence at home, Available from: http://setiathome.ssl.berkeley.edu/
The Globus Project, Available from: http://www.globus.org/
HMMER: profile HMMs for protein sequence analysis, Available from: http://hmmer.wustl.edu/
The FASTA main page, Available from: ftp://ftp.virginia.edu/pub/fasta/
mpiBLAST main page, Available from: http://mpiblast.lanl.gov/index.html
Asia Pacific BioGRID Initiative, Available from: http://www.apbionet.org/apbiogrid/
BioGRID - European grid for molecular biology, Available from: http://biogrid.icm.edu.pl/
BioGrid: Construction of a supercomputer network main page, Available from: http://www.biogrid.jp/
Moreau, L., et al.: On the Use of Agents in a Bioinformatics Grid. In: Lee, S., Sekguchi, S., Matsuoka, S., Sato, M. (eds.) Proc. of the 3rd IEEE/ACM CCGRID 2003. IEEE Computer Society, Los Alamitos (2003)
The UK MyGrid project site, Available from: http://www.mygrid.org.uk
North Carolina Bioinformatics Grid (BioGrid) web site, Available from: http://www.ncbiogrid.org
North Carolina Genomics and Bioinformatics Consortium web site, Available from: http://www.ncgbc.org
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Yang, CT., Kuo, YL., Li, KC., Gaudiot, JL. (2004). On Design of Cluster and Grid Computing Environment Toolkit for Bioinformatics Applications. In: Sen, A., Das, N., Das, S.K., Sinha, B.P. (eds) Distributed Computing - IWDC 2004. IWDC 2004. Lecture Notes in Computer Science, vol 3326. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30536-1_10
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DOI: https://doi.org/10.1007/978-3-540-30536-1_10
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