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

2009 | journal article; research paper. A publication with affiliation to the University of Göttingen.

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​Sommerfeld, Dietmar, Thomas Lingner, Mario Stanke, Burkhard Morgenstern, and Harald Richter. "AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis​." ​Future Generation Computer Systems ​25, no. 3 (2009): ​337​-345​. ​https://doi.org/10.1016/j.future.2008.05.010.

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Authors
Sommerfeld, Dietmar; Lingner, Thomas; Stanke, Mario; Morgenstern, Burkhard ; Richter, Harald
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. (C) 2008 Elsevier B.V. All rights reserved.
Issue Date
2009
Journal
Future Generation Computer Systems 
Organization
Gesellschaft für wissenschaftliche Datenverarbeitung 
ISSN
1872-7115; 0167-739X
Sponsor
German Federal Ministry of Education and Research (BMBF) [01AK803A-H]

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