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ANDY: a general, fault-tolerant tool for database searching on computer clusters.
Andrew Smith1, John-Marc Chandonia, Steven E Brenner
1Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
Bioinformatics (Oxford, England)
|January 7, 2006
Summary
ANDY (seArch coordination aND analYsis) is a Perl-based tool that efficiently distributes biological database searches across Linux computer clusters. It offers flexible operation modes and fault-tolerance, enhancing computational efficiency for large-scale analyses.
Area of Science:
- Computational Biology
- Bioinformatics
Background:
- Large-scale biological database searches require efficient computational resources.
- Existing tools may necessitate dedicated clusters, limiting flexibility.
Purpose of the Study:
- To introduce ANDY, a software package for distributed command execution on Linux clusters.
- To provide a flexible and efficient solution for managing large biological data analyses.
Main Methods:
- ANDY utilizes Perl programs and modules for task distribution.
- It supports various distributed resource management (DRM) systems and is extensible.
- Features include named pipe communication, customizable error-checking, and fault-tolerance.
Main Results:
- ANDY enables efficient execution of biological database searches across cluster nodes.
- It operates effectively on general-purpose clusters without requiring dedicated resources.
- The software demonstrates high efficiency comparable to single-purpose tools.
Conclusions:
- ANDY offers a versatile and efficient solution for distributed computing in bioinformatics.
- Its fair-use operation mode allows integration into existing cluster environments.
- The tool enhances the scalability and manageability of large biological data analyses.