Implementing a bioinformatics workflow in a parallel and distributed environment

  • Authors:

  • Ching-Lian Chua;Francis Tang;Yun-Ping Lim;Liang-Yoong Ho;Arun Krishnan

  • Affiliations:

  • Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore

  • Venue:
  • PDCAT'04 Proceedings of the 5th international conference on Parallel and Distributed Computing: applications and Technologies
  • Year:
  • 2004

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Abstract

This paper illustrates a bioinformatics workflow and its execution in a parallel and distributed environment. Our paper is organized into two main parts. The first part describes a bioinformatics study of a genome wide analysis based on full length human transcripts (cDNA information) to determine gene expression in various tissues. The second part is the execution of the workflow in a parallel and distributed environment. We show the embarrassingly parallel structure of the workflow, its implementation in a distributed cluster environment and the efficiency that can be achieved by automation of the workflow through a parallel scripting language.