Research Article

Development of distributed bioinformatics applications with GMP

  1. Bertil Schmidt1,*,
  2. Lin Feng1,
  3. Amey Laud2,
  4. Yusdi Santoso2

Article first published online: 6 JUL 2004

DOI: 10.1002/cpe.815

Issue

Concurrency and Computation: Practice and Experience

Concurrency and Computation: Practice and Experience

Special Issue: High Performance Computational Biology

Volume 16, Issue 9, pages 945–959, 10 August 2004

Additional Information

How to Cite

Schmidt, B., Feng, L., Laud, A. and Santoso, Y. (2004), Development of distributed bioinformatics applications with GMP. Concurrency Computat.: Pract. Exper., 16: 945–959. doi: 10.1002/cpe.815

Author Information

  1. 1

    School of Computer Engineering, Nanyang Technological University, Singapore 639798

  2. 2

    Helixense Pte Ltd, 73 Science Park Drive, 02-05 Science Park 1, Singapore 118254

*School of Computer Engineering, Nanyang Technological University, Singapore 639798

Publication History

  1. Issue published online: 6 JUL 2004
  2. Article first published online: 6 JUL 2004
  3. Manuscript Accepted: 8 SEP 2003
  4. Manuscript Received: 11 JUN 2003

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Keywords:

  • message passing interfaces;
  • parallel architectures for biological applications;
  • computational genomics;
  • bioinformatics systems development

Abstract

We present the design and use of gMP as a tool for developing distributed bioinformatics applications. gMP is a purely Java-based interface that adds MPI-like message-passing and collective communication to the genomics Research Network Architecture (gRNA). The gRNA is a highly programmable, modular environment specifically designed to invigorate the development of genome-centric tools for life science research. We demonstrate the development of a distributed application to detect regulatory elements using correlation with gene expression data. Its implementation with gMP leads to significant runtime savings on our distributed gRNA system. Copyright © 2004 John Wiley & Sons, Ltd.

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