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Bioinformatics Advance Access published online on March 21, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl101
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 17, 2005
Revised February 28, 2006
Accepted March 15, 2006

Applications note

XQTav: an XQuery processor for Taverna environment

Jacek Sroka 1 *, Grzegorz Kaczor 1, Jerzy Tyszkiewicz 1, and Andrzej M. Kierzek 2

1 Warsaw University, UK
2 SBMS, University of Surrey, Guildford, GU2 7XH, UK

* To whom correspondence should be addressed.
Jacek Sroka, E-mail: sroka{at}mimuw.edu.pl


  Abstract

Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the Internet. It is gaining popularity fast, due to supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav - an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query like algorithms (e.g. filters and inner joins). Moreover, XQTav may be used to automatically generate an XQuery script that is equivalent to Taverna's workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated, and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments.

Availability: XQTav is an open source software. It may be downloaded from http://xqtav.sourceforge.net. The page also contains various tutorials and examples, including the one described in this report.

Associate Editor: Martin Bishop
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