Web-Based Authoring and Secure Enactment of Bioinformatics Workflows

The recent advances in the field of bioinformatics present a number of challenges in the secure and efficient management and analysis of biological data resources. Workflow technologies aim to assist scientists and domain experts in the design of complex, long   running, data and computing intensive experiments that involve many   data processing and analysis tasks. In this paper we present a bioinformatics workflow authoring and execution environment that intends to greatly facilitate the whole lifecycle of such experiments. The main contributions of this work are a web based, easy to use, graphical workflow designer and a BPEL compliant execution environment. The ethical and security requirements when dealing with sensitive personal data that are inherent in the field of bioinformatics impose the introduction of “credentials delegation” in the workflow execution and we describe its design and implementation through bridging Grid security mechanisms with business workflows technologies.

[1]  Thomas R. Gruber,et al.  Collective knowledge systems: Where the Social Web meets the Semantic Web , 2008, J. Web Semant..

[2]  Geoffrey Fox,et al.  Special Issue: Workflow in Grid Systems , 2006, Concurr. Comput. Pract. Exp..

[3]  Ian J. Taylor,et al.  Distributed computing with Triana on the Grid , 2005, Concurr. Pract. Exp..

[4]  Irfan-Ullah Awan,et al.  Analysis of grid service composition with BPEL4WS , 2004, 18th International Conference on Advanced Information Networking and Applications, 2004. AINA 2004..

[5]  Frank Leymann,et al.  Choreography for the Grid: towards fitting BPEL to the resource framework , 2006, Concurr. Comput. Pract. Exp..

[6]  Sanjiva Weerawarana,et al.  Unraveling the Web services web: an introduction to SOAP, WSDL, and UDDI , 2002, IEEE Internet Computing.

[7]  Aleksander Slomiski,et al.  On using BPEL extensibility to implement OGSI and WSRF Grid workflows , 2006, Concurr. Comput. Pract. Exp..

[8]  Natawut Nupairoj,et al.  The BPEL orchestrating framework for secured grid services , 2005, International Conference on Information Technology: Coding and Computing (ITCC'05) - Volume II.

[9]  Frank Leymann,et al.  Choreography for the Grid: towards fitting BPEL to the resource framework: Research Articles , 2006 .

[10]  Ian T. Foster,et al.  Security for Grid services , 2003, High Performance Distributed Computing, 2003. Proceedings. 12th IEEE International Symposium on.

[11]  Bertram Ludäscher,et al.  Kepler: an extensible system for design and execution of scientific workflows , 2004, Proceedings. 16th International Conference on Scientific and Statistical Database Management, 2004..

[12]  Stefan Rüping,et al.  GridR: An R-Based Grid-Enabled Tool for Data Analysis in ACGT Clinico-Genomics Trials , 2007, Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007).

[13]  Kenneth J. Turner,et al.  Orchestrating Grid Services using BPEL and Globus Toolkit 4 , 2006 .

[14]  José Francisco Aldana Montes,et al.  Intelligent client for integrating bioinformatics services , 2006, Bioinform..

[15]  Hans H. Kron,et al.  Programming-in-the-Large Versus Programming-in-the-Small , 1975, IEEE Transactions on Software Engineering.

[16]  Edward A. Lee,et al.  Implementing BPEL4WS: the architecture of a BPEL4WS implementation: Research Articles , 2006 .

[17]  Manolis Tsiknakis,et al.  A Semantic Grid Infrastructure Enabling Integrated Access and Analysis of Multilevel Biomedical Data in Support of Postgenomic Clinical Trials on Cancer , 2008, IEEE Transactions on Information Technology in Biomedicine.

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

[19]  Francisco Curbera,et al.  Web Services Business Process Execution Language Version 2.0 , 2007 .

[20]  Wendy Hall,et al.  The Semantic Web Revisited , 2006, IEEE Intelligent Systems.

[21]  Jano I. van Hemert,et al.  Scientific Workflow: A Survey and Research Directions , 2007, PPAM.

[22]  Ivan Janciak,et al.  Workflow enactment engine for WSRF-compliant services orchestration , 2008, 2008 9th IEEE/ACM International Conference on Grid Computing.

[23]  I. Foster,et al.  The grid: computing without bounds. , 2003, Scientific American.

[24]  Liang Chen,et al.  Grid Service Orchestration Using the Business Process Execution Language (BPEL) , 2005, Journal of Grid Computing.

[25]  Edward A. Lee,et al.  CONCURRENCY AND COMPUTATION: PRACTICE AND EXPERIENCE Concurrency Computat.: Pract. Exper. 2000; 00:1–7 Prepared using cpeauth.cls [Version: 2002/09/19 v2.02] Taverna: Lessons in creating , 2022 .

[26]  Thomas Friese,et al.  Grid Workflow Modelling Using Grid-Specific BPEL Extensions , 2007 .

[27]  Norman W. Paton,et al.  The design and implementation of Grid database services in OGSA‐DAI , 2005, Concurr. Pract. Exp..

[28]  David Meredith,et al.  Evaluation of BPEL to Scientific Workflows , 2006, Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06).

[29]  Nikolaus Forgó,et al.  A data protection framework for trans-European genetic research projects. , 2008, Studies in health technology and informatics.

[30]  Rajkumar Buyya,et al.  A Taxonomy of Workflow Management Systems for Grid Computing , 2005, Proceedings of the 38th Annual Hawaii International Conference on System Sciences.