AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis

  • Authors:

  • Dietmar Sommerfeld;Thomas Lingner;Mario Stanke;Burkhard Morgenstern;Harald Richter

  • Affiliations:

  • Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen, Am Fassberg, 37077 Göttingen, Germany;Department of Bioinformatics, University of Göttingen, 37077 Göttingen, Germany;Department of Bioinformatics, University of Göttingen, 37077 Göttingen, Germany;Department of Bioinformatics, University of Göttingen, 37077 Göttingen, Germany;Department of Informatics, Clausthal University of Technology, 38678 Clausthal-Zellerfeld, Germany

  • Venue:
  • Future Generation Computer Systems
  • Year:
  • 2009

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Abstract

In past years, researchers from many domains have discovered Grid technology which opens up new possibilities in solving problems that are difficult to handle with traditional cluster computing. With the rapidly increasing number of partially or completely sequenced genomes, computational genome annotation is a particularly challenging task in computational biology. In this paper, we describe how we adapted the gene-finding tool AUGUSTUS to Grid computing in the context of the German MediGRID project. The gridification process starts with providing security requirements and running the application manually using Grid middleware. Afterwards, the application is described as a workflow of successive program executions, which are automatically distributed to appropriate Grid resources by a workflow engine. Finally, we show how a convenient graphical user interface for end users is created by means of a portal framework.