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Open Access Publications from the University of California

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

  • Author(s): Smith, Andrew
  • Chandonia, John-Marc
  • Brenner, Steven E.
  • et al.

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; this site also contains supplemental data and figures and amore detailed overview of the software.

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