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Bioinformatics Advance Access originally published online on April 1, 2004
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Bioinformatics 20(13) © Oxford University Press 2004; all rights reserved.

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 and A. Gupta 2

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

Received on July 24, 2003; revised on February 27, 2004; accepted on March 1, 2004
Advance Access Publication April 1, 2004

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) and Kweelt implementation of XQuery (http://kweelt.sourceforge.net/).

Contact: monica.chagoyen{at}cnb.uam.es

* To whom correspondence should be addressed.


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