A new language to define bioinformatics workflows using Web services

Workflow systems provide a perfect fit for the explorative research of bioinformaticians. These systems can help bioinformaticians to design and run their experiments and to automatically capture and store the data generated at runtime. In this paper we present a new language (workflow representation) that enables the design of high-level workflow models. Such a workflow system will be much easier in use and will better suit the bioinformaticians needs. In the paper, we describe the overall framework of our approach and provide a detailed description of the techniques proposed. Finally, the usefulness of our approach is demonstrated through a bioinformatics case study.

[1]  Anton Nijholt,et al.  Bringing Hollywood to the Driving School: Dynamic Scenario Generation in Simulations and Games , 2005, INTETAIN.

[2]  Ignacio Marín,et al.  Ancient Origin of the Parkinson Disease Gene LRRK2 , 2008, Journal of Molecular Evolution.

[3]  Heidi J. C. Ellis,et al.  Conceptual-level workflow modeling of scientific experiments using NMR as a case study , 2007, BMC Bioinformatics.

[4]  James F. Brinkley,et al.  Issues in biomedical research data management and analysis: needs and barriers. , 2007, Journal of the American Medical Informatics Association : JAMIA.

[5]  Hoda M. O. Mokhtar,et al.  A Flexible Tool for Web Service Selection in Service Oriented Architecture , 2011 .

[6]  Carole A. Goble,et al.  The myGrid ontology: bioinformatics service discovery , 2007, Int. J. Bioinform. Res. Appl..

[7]  Maria Luisa Villani,et al.  An approach for QoS-aware service composition based on genetic algorithms , 2005, GECCO '05.

[8]  Jos de Bruijn,et al.  Web Service Modeling Ontology , 2005, Appl. Ontology.

[9]  Hong Qing Yu,et al.  Non-functional Property based service selection: A survey and classification of approaches , 2008 .

[10]  Wil M. P. van der Aalst,et al.  Worklets: A Service-Oriented Implementation of Dynamic Flexibility in Workflows , 2006, OTM Conferences.

[11]  Tao Xu,et al.  Pegasys: software for executing and integrating analyses of biological sequences , 2004, BMC Bioinformatics.

[12]  Carole Goble,et al.  BioCatalogue: A Curated Web Service Registry For The Life Science Community , 2009 .

[13]  Mark D. Wilkinson,et al.  BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..

[14]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[15]  Pieter B. T. Neerincx.  Web services for transcriptomics , 2009 .