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Bioinformatics Advance Access published online on April 1, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth209
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 24, 2003
Revised February 27, 2004
Accepted March 1, 2004

Article

‘Designing and executing scientific workflows with a programmable integrator’

M. Chagoyen 1, M. E. Kurul 2, P. A. De-Alarcón 3, J. M. Carazo 1, A. Gupta 2*

1 Biocomputing Unit, Centro Nacional de Biotecnología, Madrid 28049, Spain
2 San Diego Supercomputer Center - U.C. San Diego, La Jolla CA 92093-0505, USA
3 Integromics S.L. - Parque Científico Madrid, Madrid 28049, Spain

* To whom correspondence should be addressed. E-mail: gupta{at}sdsc.edu.


  Abstract

Motivation: As in many other fields of science, computational methods in molecular biology need to intersperse information access and algorithm execution in a computational workflow. Users often find difficulties when transferring data between data sources and applications. In most cases there is no standard solution for workflow design and execution and tailored scripting mechanisms are implemented in a case by case basis.

Results: In this paper we present a general purpose "programmable integrator" that can access information from a variety of sources in a coordinated manner. Its usefulness in complex bioinformatics applications is claimed and supported by some application examples.

Availability: Tools are freely available to non-profit educations and research institutions. Usage by commercial organizations requires a license agreement. Software requirements: Java v1.3 (http://java.sun.com), Xerces XML Parser (http://xml.apache.org/xerces-j), Kweelt implementation of XQuery (http://kweelt.sourceforge.net/).


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