Scientific workflow systems - Can one size fit all?

2008 Cairo International Biomedical Engineering Conference, CIBEC 2008

Volumn , Issue , 2008, Pages

  Curcin, V ^a   Ghanem, M ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION TASKS; COMPUTATIONAL RESOURCES; CONTROL FLOWS; DATA FLOWS; LIFE SCIENCE; SCIENTIFIC DATUM; SCIENTIFIC RESEARCHES; SCIENTIFIC WORKFLOW; STATE-OF-THE ARTS; WORK-FLOW SYSTEMS;

BIOINFORMATICS; BIOMEDICAL ENGINEERING; MANAGEMENT;

ACCESS CONTROL;

EID: 78650760428     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/CIBEC.2008.4786077     Document Type: Conference Paper

References (38)

1. M. Ghanem, V. Curcin, P. Wendel, and Y. Guo, "Building and using analytical workflows in discovery net," in Data mining on the Grid, W. Dubitzky, Ed. John Wiley and Sons, 2008.
2. D. Hull, K. Wolstencroft, R. Stevens, C. Goble, M. R. Pocock, P. Li, and T. Oinn, "Taverna: A tool for building and running workflows of services," Nucleic Acids Research, vol. 34, pp. W729-W732, 2006, web Server Issue.
3. I. Taylor, M. Shields, I. Wang, and A. Harrison, "Visual Grid Workflow in Triana," Journal of Grid Computing, vol. 3, no. 3-4, pp. 153-169, September 2005. [Online]. Available: http://www.springerlink.com/ openurl.asp?genre=article&issn= &volume=3&issue=3&spage=153
4. B. Ludäscher, I. Altintas, C. Berkley, D. Higgins, E. Jaeger, M. Jones, E. A. Lee, J. Tao, and Y. Zhao, "Scientific workflow management and the kepler system: Research articles," Concurr. Comput. : Pract. Exper., vol. 18, no. 10, pp. 1039-1065, 2006.
5. W. van der Aalst and A. Hofstede, "Yawl: Yet another workflow language," 2002. [Online]. Available: citeseer.ist.psu.edu/ vanderaalst03yawl.html
6. T. Andrews, F. Curbera, H. Dholakia, Y. Goland, J. Klein, F. Leymann, K. Liu, D. Roller, D. Smith, S. Thatte, I. Trickovic, and S. Weerawarana, "Business process execution language for web services version 1.1," http://www-128.ibm.com/developerworks/library/specification/wsbpel/, BEA Systems, IBM, Microsoft, SAP, Siebel Systems., Tech. Rep., 2003.
7. J. Bradley, C. Brown, B. Carpenter, V. Chang, J. Crisp, S. Crouch, D. D. Roure, S. Newhouse, G. Li, J. Papay, C. Walker, and A. Wookey, "The omii software distribution," in All Hands Meeting 2006, 2006, pp. 748-753. [Online]. Available: http://eprints.ecs.soton.ac.uk/13407/
8. A. Rowe, D. Kalaitzopoulos, M. Osmond, M. Ghanem, and Y. Guo, "The discovery net system for high throughput bioinformatics," Bioinformatics, vol. 19, no. 90001, pp. 225i-231, 2003.
9. M. Ghanem, Y. Guo, H. Lodhi, and Y. Zhang, "Automatic scientific text classification using local patterns: KDD CUP 2002 (task 1)," SIGKDD Explor. Newsl., vol. 4, no. 2, pp. 95-96, December 2002.
10. V. Curcin, M. Ghanem, Y. Guo, A. Rowe, W. He, H. Pei, L. Qiang, and Y. Li, "It service infrastructure for integrative systems biology," in SCC '04: Proceedings of the 2004 IEEE International Conference on Services Computing. Washington, DC, USA: IEEE Computer Society, 2004, pp. 123-131.
11. M. Richards, M. Ghanem, M. Osmond, Y. Guo, and J. Hassard, "Gridbased analysis of air pollution data," Ecological Modelling, vol. 194, pp. 274-286, 2006.
12. Y. Guo, J. G. Liu, M. Ghanem, K. Mish, V. Curcin, C. Haselwimmer, D. Sotiriou, K. K. Muraleetharan, and L. Taylor, "Bridging the macro and micro: A computing intensive earthquake study using discovery net," in SC '05: Proceedings of the 2005 ACM/IEEE conference on Supercomputing. Washington, DC, USA: IEEE Computer Society, 2005, p. 68.
13. (2008) Inforsense ltd. [Online]. Available: http://www.inforsense.com/
14. C. Upstill and M. Boniface, "Simdat," CTWatch Quarterly, vol. 1, no. 4, pp. 16-20, November 2005. [Online]. Available: http://eprints.ecs.soton.ac.uk/11622/
15. J. Syed, M. Ghanem, and Y. Guo, "Discovery processes: Representation and reuse," in Proceedings of First UK e-Science All-hands Conference, Sheffield, UK, 2002.
16. M. Ghanem, A. Chortaras, and Y. Guo, "Web Service programming for biomedical text mining," in SIGIR Workshop on Search and Discovery in Bioinformatics held in conjunction with the 27th Annual International ACM SIGIR Conference, Sheffield, UK, July 2004. [Online]. Available: http://pubs.doc.ic.ac.uk/web-service-text-mining/
17. T. Oinn, M. Addis, J. Ferris, D. Marvin, M. Greenwood, C. Goble, A. Wipat, P. Li, and T. Carver, "Delivering web service coordination capability to users," in WWW Alt. '04: Proceedings of the 13th international World Wide Web conference on Alternate track papers & posters. New York, NY, USA: ACM, 2004, pp. 438-439.
18. (2008) Freefluo enactment engine. [Online]. Available: http://freefluo.sourceforge.net
19. S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. G. Tate, S. S. Velankar, A. Golovin, K. Henrick, P. Rice, P. Stoehr, and R. Lopez, "Soap-based services provided by the european bioinformatics institute." Nucleic Acids Research, vol. 33, no. Web-Server-Issue, pp. 25-28, 2005.
20. K. Michalickova, G. D. Bader, M. Dumontier, H. Lieu, D. Betel, R. Isserlin, and C. W. V. Hogue, "Seqhound: biological sequence and structure database as a platform for bioinformatics research." BMC Bioinformatics, vol. 3, p. 32, 2002.
21. I. J. Taylor, E. Deelman, and D. B. Gannon, Workflows for e-Science: Scientific Workflows for Grids. Springer, December 2006.
22. R. Balasubramanian, S. Babak, D. Churches, and T. Cokelaer, "Geo600 online detector characterization system," Classical and Quantum Gravity, vol. 22, p. 4973, 2005. [Online]. Available: http://www.citebase. org/abstract?id=oai:arXiv.org:gr-qc/0504140
23. G. Allen, K. Davis, T. Dramlitsch, T. Goodale, I. Kelley, G. Lanfermann, J. Novotny, T. Radke, K. Rasul, M. Russell, E. Seidel, and O. Wehrens, "The gridlab grid application toolkit," in HPDC '02: Proceedings of the 11 th IEEE International Symposium on High Performance Distributed Computing HPDC-11 20002 (HPDC'02). Washington, DC, USA: IEEE Computer Society, 2002, p. 411.
24. I. Taylor, M. Shields, I. Wang, and O. Rana, "Triana Applications within Grid Computing and Peer to Peer Environments," Journal of Grid Computing, vol. 1, no. 2, pp. 199-217, 2003. [Online]. Available: http://journals.kluweronline.com/article.asp?PIPS=5269002
25. I. Taylor, M. Shields, I. Wang, and A. Harrison, "The Triana Workflow Environment: Architecture and Applications," in Workflows for e-Science, I. Taylor, E. Deelman, D. Gannon, and M. Shields, Eds. Secaucus, NJ, USA: Springer, New York, 2007, pp. 320-339.
26. R. Winder, "Hello groovy!" CVU, vvol. 18, no. 3, pp. 3-7, 2006.
27. T. Boudreau, J. Glick, and V. Spurlin, NetBeans: The Definitive Guide. Sebastopol, CA, USA: O'Reilly & Associates, Inc., 2002.
28. C. Brooks, E. Lee, X. Liu, S. Neuendorffer, and H. Z. e. Y. Zhao, "Heterogeneous concurrent modeling and design in java (volume 2: Ptolemy ii software architecture)," EECS Dept., UC Berkeley, Tech. Rep. 22, July 2005. [Online]. Available: http://chess.eecs.berkeley.edu/pubs/63.html
29. E. A. Lee and Y. Xiong, "A behavioral type system and its application in ptolemy ii," Form. Asp. Comput., vol. 16, no. 3, pp. 210-237, 2004.
30. T. Nagatani, "Interaction between buses and passengers on a bus route," Physica A Statistical Mechanics and its Applications, vol. 296, pp., Jul. 2001.
31. A. Goderis, C. Brooks, I. Altintas, E. A. Lee, and C. Goble, "Heterogeneous composition of models of computation," EECS Department, University of California, Berkeley, Tech. Rep. UCB/EECS-2007-139, November 2007.
32. Y. Chen and van Aalst, "On scientific workflows," IEEE Computer Society's Technical Committee for Scalable Computing, 2007. [Online]. Available: citeseer.ist.psu.edu/plotkin03origins.html
33. W. M. P. van der Aalst, A. H. M. ter Hofstede, B. Kiepuszewski, and A. P. Barros, "Workflow patterns," Distributed and Parallel Databases, vol. 14, pp. 5-51, 2003.
34. M. Addis, J. Ferris, M. Greenwood, P. Li, D. Marvin, T. Oinn, and A. Wipat, "Experiences with e-science workflow specification and enactment in bioinformatics," in e-Science All Hands Meeting 2003, S. Cox, Ed., 2003, pp. 459-466.
35. B. Wassermann, W. Emmerich, B. Butchart, N. Cameron, L. Chen, and J. Patel, "Sedna: A BPEL-based environment for visual scientific workflow modelling," in Workflows for eScience - Scientific Workflows for Grids, I. Taylor, E. Deelman, D. Gannon, and M. Shields, Eds. Springer Verlag, 2006.
36. A. Slominsky, "Adapting BPEL to Scientific Workflows," in Workflows for e-Science, I. Taylor, E. Deelman, D. Gannon, and M. Shields, Eds. Springer, New York, 2007, pp. 208-226.
37. B. Wassermann, W. Emmerich, B. Butchart, N. Cameron, L. Chen, and J. Patel, "Sedna: A BPEL-based environment for visual scientific workflow modelling," in Workflows for eScience - Scientific Workflows for Grids, I. Taylor, E. Deelman, D. Gannon, and M. Shields, Eds. Springer Verlag, 2006.
38. A. Goderis, C. Brooks, I. Altintas, E. A. Lee, and C. A. Goble, "Composing different models of computation in kepler and ptolemy ii." in International Conference on Computational Science (3), ser. Lecture Notes in Computer Science, Y. Shi, G. D. van Albada, J. Dongarra, and P. M. A. Sloot, Eds., vol. 4489. Springer, 2007, pp. 182-190.