Paper Info
Title
Combining a high-throughput bioinformatics grid and bioinformatics web services
Abstract
We have created a high-throughput grid for biological sequence analysis, which is freely accessible via bioinformatics Web services. The system allows the execution of computationally intensive sequence alignment algorithms, such as Smith-Waterman or hidden Markov model searches, with speedups up to three orders of magnitude over single-CPU installations. Users around the world can now process highly sensitive sequence alignments with a turnaround time similar to that of BLAST tools. The grid combines high-throughput accelerators at two bioinformatics facilities in different geographical locations. The tools include TimeLogic DeCypher boards, a Paracel GeneMatcher2 accelerator, and Paracel BlastMachines. The Sun N1 Grid Engine software performs distributed resource management. Clients communicate with the grid through existing open BioMOBY Web services infrastructure. We also illustrate bioinformatics grid strategies for distributed load balancing, and report several nontrivial technical solutions that may serve as templates for adaptation by other bioinformatics groups.
Year
DOI
Venue
2006
10.1007/978-3-540-69968-2_1
GCCB
Keywords
Field
DocType
sequence alignment,sequence analysis,high throughput,web service,software performance,load balance,hidden markov model
Grid computing,Computer science,Load balancing (computing),Software,Turnaround time,Smith–Waterman algorithm,Semantic grid,Bioinformatics,Web service,Grid,Distributed computing
Conference
Volume
ISSN
Citations 
4360
0302-9743
0
PageRank 
References 
Authors
0.34
13
6
Name
Order
Citations
PageRank
Chunyan Wang100.34
Paul M. K. Gordon2957.51
Andrei L. Turinsky3846.13
Jason Burgess400.34
Terry Dalton500.34
Christoph W. Sensen6978.25