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Bioinformatics Advance Access originally published online on March 19, 2008
Bioinformatics 2008 24(9):1221-1222; doi:10.1093/bioinformatics/btn095
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Integrating ARC grid middleware with Taverna workflows

Hajo N. Krabbenhöft , Steffen Möller and Daniel Bayer *

Institute for Neuro- and Bioinformatics, University of Lübeck, 23538 Lübeck, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: This work presents two independent approaches for a seamless integration of computational grids with the bioinformatics workflow suite Taverna. These are supported by a unique relational database to link applications with grid resources and presents those as workflow elements. A web portal facilitates its collaborative maintenance. The first approach implements a gateway service to handle authentication certificates and all communication with the grid. It reads the database to spawn web services for workflow elements which are in turn used by Taverna. The second approach lets Taverna communicate with the grid on its own, by means of a newly developed plug-in. It reads the database and executes the needed tasks directly on the grid. While the gateway service is non-intrusive, the plug-in has technical advantages, e.g. by allowing data to remain on the grid while being passed between workflow elements.

Availability: http://grid.inb.uni-luebeck.de/

Contact: bayer{at}inb.uni-luebeck.de

Associate Editor: Alfonso Valencia

Received on January 21, 2008; revised on February 19, 2008; accepted on March 6, 2008

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