Table of Contents
Computational Biology Journal
Volume 2013 (2013), Article ID 707540, 12 pages
http://dx.doi.org/10.1155/2013/707540
Research Article

SCBI_MapReduce, a New Ruby Task-Farm Skeleton for Automated Parallelisation and Distribution in Chunks of Sequences: The Implementation of a Boosted Blast+

1Supercomputación y Bioinformática-Plataforma Andaluza de Bioinformática (SCBI-PAB), Universidad de Málaga, 29071 Málaga, Spain
2Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, 29071 Málaga, Spain
3Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, 29071 Málaga, Spain

Received 21 June 2013; Revised 18 September 2013; Accepted 19 September 2013

Academic Editor: Ivan Merelli

Copyright © 2013 Darío Guerrero-Fernández et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Current genomic analyses often require the managing and comparison of big data using desktop bioinformatic software that was not developed regarding multicore distribution. The task-farm SCBI_MAPREDUCE is intended to simplify the trivial parallelisation and distribution of new and legacy software and scripts for biologists who are interested in using computers but are not skilled programmers. In the case of legacy applications, there is no need of modification or rewriting the source code. It can be used from multicore workstations to heterogeneous grids. Tests have demonstrated that speed-up scales almost linearly and that distribution in small chunks increases it. It is also shown that SCBI_MAPREDUCE takes advantage of shared storage when necessary, is fault-tolerant, allows for resuming aborted jobs, does not need special hardware or virtual machine support, and provides the same results than a parallelised, legacy software. The same is true for interrupted and relaunched jobs. As proof-of-concept, distribution of a compiled version of BLAST+ in the SCBI_DISTRIBUTED_BLAST gem is given, indicating that other blast binaries can be used while maintaining the same SCBI_DISTRIBUTED_BLAST code. Therefore, SCBI_MAPREDUCE suits most parallelisation and distribution needs in, for example, gene and genome studies.