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Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Tampa, Florida
November 11-November 17
ISBN: 0-7695-2700-0
ASCII Text
x 
 
Mark K. Gardner, Wu-chun Feng, Jeremy Archuleta, Heshan Lin, Xiaosong Ma, "Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications," SC Conference, pp. 22, Proceedings of the 2006 ACM/IEEE conference on Supercomputing, 2006.
 
 
BibTex
x
 
@article{ 10.1109/SC.2006.46,
author = {Mark K. Gardner and Wu-chun Feng and Jeremy Archuleta and Heshan Lin and Xiaosong Ma},
title = {Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications},
journal ={SC Conference},
volume = {0},
year = {2006},
isbn = {0-7695-2700-0},
pages = {22},
doi = {http://doi.ieeecomputersociety.org/10.1109/SC.2006.46},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - SC Conference
TI - Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications
SN - 0-7695-2700-0
SP
EP
A1 - Mark K. Gardner,
A1 - Wu-chun Feng,
A1 - Jeremy Archuleta,
A1 - Heshan Lin,
A1 - Xiaosong Ma,
PY - 2006
KW - bioinformatics
KW - BLAST
KW - sequence search
KW - grid computing
KW - cluster computing
KW - optical networking
KW - scheduling
KW - fault tolerance
KW - scalability
KW - agile development
KW - scripting
VL - 0
JA - SC Conference
ER -
 
Mark K. Gardner, Virginia Tech
Wu-chun Feng, Virginia Tech
Jeremy Archuleta, University of Utah
Heshan Lin, North Carolina State University
Xiaosong Ma, North Carolina State University

The Basic Local Alignment Search Tool (BLAST) allows bioinformaticists to characterize an unknown sequence by comparing it against a database of known sequences. The similarity between sequences enables biologists to detect evolutionary relationships and infer biological properties of the unknown sequence.

mpiBLAST, our parallel BLAST, decreases the search time of a 300KB query on the current NT database from over two full days to under 10 minutes on a 128- processor cluster and allows larger query files to be compared. Consequently, we propose to compare the largest query available, the entire NT database, against the largest database available, the entire NT database. The result of this comparison will provide critical information to the biology community, including insightful evolutionary, structural, and functional relationships between every sequence and family in the NT database.

Preliminary projections indicated that to complete the above task in a reasonable length of time required more processors than were available to us at a single site. Hence, we assembled GreenGene, an ad-hoc grid that was constructed "on the fly" from donated computational, network, and storage resources during last year's SC|05. GreenGene consisted of 3048 processors from machines that were distributed across the United States. This paper presents a case study of mpiBLAST on GreenGene - specifically, a pre-run characterization of the computation, the hardware and software architectural design, experimental results, and future directions.

Index Terms:
bioinformatics, BLAST, sequence search, grid computing, cluster computing, optical networking, scheduling, fault tolerance, scalability, agile development, scripting
Citation:
Mark K. Gardner, Wu-chun Feng, Jeremy Archuleta, Heshan Lin, Xiaosong Ma, "Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications," sc, pp.22, Proceedings of the 2006 ACM/IEEE conference on Supercomputing, 2006
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