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Bioinformatics Advance Access published online on January 5, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk020
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received August 22, 2005
Revised November 29, 2005
Accepted December 20, 2005

Applications note

ANDY: a general, fault-tolerant tool for database searching on computer clusters

Andrew Smith 1, John-Marc Chandonia 2, and Steven E. Brenner 3 *

1 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Current Address: Department of Computer Science, Yale University, New Haven, CT 06520, USA
2 Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Berkeley Structural Genomics Center, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

* To whom correspondence should be addressed.
Steven E. Brenner, E-mail: brenner{at}compbio.berkeley.edu


  Abstract

Summary: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used Distributed Resource Management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms.

Availability: ANDY is freely available and may be obtained from http://compbio.berkeley.edu/proj/andy; this site also contains supplemental data and figures and a more detailed overview of the software.


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