CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

Tan, Wei; Madduri, Ravi; Nenadic, Alexandra; Soiland-Reyes, Stian; Sulakhe, Dinanath; Foster, Ian; Goble, Carole A.

doi:10.1186/1471-2105-11-542

Title: CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

Journal Article · Tue Nov 02 00:00:00 EDT 2010 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-11-542· OSTI ID:1626274

Tan, Wei ^[1]; Madduri, Ravi ^[2]; Nenadic, Alexandra ^[3]; Soiland-Reyes, Stian ^[3]; Sulakhe, Dinanath ^[1]; Foster, Ian ^[2]; Goble, Carole A. ^[3]

Univ. of Chicago, IL (United States). Argonne National Lab. (ANL). Computation Inst.
Univ. of Chicago, IL (United States). Argonne National Lab. (ANL). Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
Univ. of Manchester (United Kingdom). School of Computer Science

Background: In biological and medical domain, the use of web services made the data and computation functionality accessible in a unified manner, which helped automate the data pipeline that was previously performed manually. Workflow technology is widely used in the orchestration of multiple services to facilitate insilico research. Cancer Biomedical Informatics Grid (caBIG) is an information network enabling the sharing of cancer research related resources and caGrid is its underlying service-based computation infrastructure. CaBIG requires that services are composed and orchestrated in a given sequence to realize data pipelines, which are often called scientific workflows. Results: CaGrid selected Taverna as its workflow execution system of choice due to its integration with web service technology and support for a wide range of web services, plug-in architecture to cater for easy integration of third party extensions, etc. The caGrid Workflow Toolkit (or the toolkit for short), an extension to the Taverna workflow system, is designed and implemented to ease building and running caGrid workflows. It provides users with support for various phases in using workflows: service discovery, composition and orchestration, data access, and secure service invocation, which have been identified by the caGrid community as challenging in a multiinstitutional and cross-discipline domain. Conclusions: By extending the Taverna Workbench, caGrid Workflow Toolkit provided a comprehensive solution to compose and coordinate services in caGrid, which would otherwise remain isolated and disconnected from each other. Using it users can access more than 140 services and are offered with a rich set of features including discovery of data and analytical services, query and transfer of data, security protections for service invocations, state management in service interactions, and sharing of workflows, experiences and best practices. The proposed solution is general enough to be applicable and reusable within other service-computing infrastructures that leverage similar technology stack.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1626274

Journal Information:: BMC Bioinformatics, Vol. 11, Issue 1; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (23)

CDK-Taverna: an open workflow environment for cheminformatics Kuhn, Thomas; Willighagen, Egon L.; Zielesny, Achim BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-159	journal	January 2010
The design and realisation of the $^{my}$Experiment Virtual Research Environment for social sharing of workflows De Roure, David; Goble, Carole; Stevens, Robert Future Generation Computer Systems, Vol. 25, Issue 5, p. 561-567 https://doi.org/10.1016/j.future.2008.06.010	journal	May 2009
Cancer Informatics Vision: caBIG ^™ Von Eschenbach, Andrew C.; Buetow, Kenneth Cancer Informatics, Vol. 2 https://doi.org/10.1177/117693510600200013	journal	January 2006
e-Science, caGrid, and Translational Biomedical Research Saltz, J.; Kurc, T.; Hastings, S. Computer, Vol. 41, Issue 11 https://doi.org/10.1109/MC.2008.459	journal	November 2008
Swift: Fast, Reliable, Loosely Coupled Parallel Computation Zhao, Yong; Hategan, Mihael; Clifford, Ben 2007 IEEE Congress on Services (Services 2007) https://doi.org/10.1109/SERVICES.2007.63	conference	July 2007
Composition as a service [Web-Scale Workflow Blake, M. B.; Tan, Wei; Rosenberg, F. IEEE Internet Computing, Vol. 14, Issue 1, p. 78-82 https://doi.org/10.1109/MIC.2010.2	journal	January 2010
Taverna: a tool for building and running workflows of services Hull, D.; Wolstencroft, K.; Stevens, R. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl320	journal	July 2006
Workflows for e-Science Taylor, Ian J.; Deelman, Ewa; Gannon, Dennis B. Springer London https://doi.org/10.1007/978-1-84628-757-2	book	January 2007
Pegasus: A Framework for Mapping Complex Scientific Workflows onto Distributed Systems Deelman, Ewa; Singh, Gurmeet; Su, Mei-Hui Scientific Programming, Vol. 13, Issue 3 https://doi.org/10.1155/2005/128026	journal	January 2005
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid Saltz, J.; Oster, S.; Hastings, S. Bioinformatics, Vol. 22, Issue 15 https://doi.org/10.1093/bioinformatics/btl272	journal	June 2006
Scientific workflow management and the Kepler system Ludäscher, Bertram; Altintas, Ilkay; Berkley, Chad Concurrency and Computation: Practice and Experience, Vol. 18, Issue 10 https://doi.org/10.1002/cpe.994	journal	January 2006
The Globus Toolkit 4 Sotomayor, Borja; Childers, Lisa Globus® Toolkit 4 https://doi.org/10.1016/B978-012369404-1/50008-8	book	January 2006
Taverna: lessons in creating a workflow environment for the life sciences Oinn, Tom; Greenwood, Mark; Addis, Matthew Concurrency and Computation: Practice and Experience, Vol. 18, Issue 10 https://doi.org/10.1002/cpe.993	journal	January 2006
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning Shipp, Margaret A.; Ross, Ken N.; Tamayo, Pablo Nature Medicine, Vol. 8, Issue 1 https://doi.org/10.1038/nm0102-68	journal	January 2002
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data Li, Peter; Castrillo, Juan I.; Velarde, Giles BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-334	journal	August 2008
Service-Oriented Science Foster, I. Science, Vol. 308, Issue 5723 https://doi.org/10.1126/science.1110411	journal	May 2005
Globus Toolkit Version 4: Software for Service-Oriented Systems Foster, Ian Journal of Computer Science and Technology, Vol. 21, Issue 4 https://doi.org/10.1007/s11390-006-0513-y	journal	July 2006
Combining the Power of Taverna and caGrid: Scientific Workflows that Enable Web-Scale Collaboration Tan, Wei; Foster, Ian; Madduri, Ravi IEEE Internet Computing, Vol. 12, Issue 6 https://doi.org/10.1109/MIC.2008.120	journal	November 2008
Modeling and Managing State in Distributed Systems: The Role of OGSI and WSRF Foster, I.; Czajkowski, K.; Ferguson, D. E. Proceedings of the IEEE, Vol. 93, Issue 3 https://doi.org/10.1109/JPROC.2004.842766	journal	March 2005
BioCatalogue: a universal catalogue of web services for the life sciences Bhagat, J.; Tanoh, F.; Nzuobontane, E. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq394	journal	May 2010
Security for Grid services Welch, V.; Siebenlist, F.; Foster, I. High Performance Distributed Computing, 2003. Proceedings. 12th IEEE International Symposium on https://doi.org/10.1109/hpdc.2003.1210015	conference
Trident: Scientific Workflow Workbench for Oceanography Barga, R. S.; Jackson, J.; Araujo, N. 2008 IEEE Congress on Services Part 1 (SERVICES-1), 2008 IEEE Congress on Services - Part I https://doi.org/10.1109/services-1.2008.101	conference	July 2008
Sharing Data and Analytical Resources Securely in a Biomedical Research Grid Environment Langella, S.; Hastings, S.; Oster, S. Journal of the American Medical Informatics Association, Vol. 15, Issue 3 https://doi.org/10.1197/jamia.m2662	journal	May 2008

Cited By (3)

PAV ontology: provenance, authoring and versioning Ciccarese, Paolo; Soiland-Reyes, Stian; Belhajjame, Khalid Journal of Biomedical Semantics, Vol. 4, Issue 1 https://doi.org/10.1186/2041-1480-4-37	journal	January 2013
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud Wolstencroft, Katherine; Haines, Robert; Fellows, Donal Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt328	journal	May 2013
SIDECACHE: Information access, management and dissemination framework for web services Doderer, Mark S.; Burkhardt, Cory; Robbins, Kay A. BMC Research Notes, Vol. 4, Issue 1 https://doi.org/10.1186/1756-0500-4-182	journal	June 2011

Similar Records

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

Journal Article · Sat Mar 01 00:00:00 EST 2008 · J. Am. Inform. Assoc. · OSTI ID:1626274

Oster, S; Langella, S; Hastings, S; +10 more

Domain-Specific Languages for Composing Signature Discovery Workflows

Conference · Tue Oct 23 00:00:00 EDT 2012 · OSTI ID:1626274

Jacob, Ferosh; Gray, Jeff; Wynne, Adam S.; +2 more

Domain-Specific Languages For Developing and Deploying Signature Discovery Workflows

Journal Article · Mon Dec 02 00:00:00 EST 2013 · Computing in Science & Engineering, 16(1):52-64 · OSTI ID:1626274

Jacob, Ferosh; Wynne, Adam S.; Liu, Yan; +1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Mathematical & Computational Biology

Title: CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid

Citation Formats

References (23)

Cited By (3)

Similar Records

Related Subjects