E-Biology Workflows with Calvin

  • Markus Held
  • Wolfgang Blochinger
  • Moritz Werning
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5802)

Abstract

Web portals enable sharing, execution and monitoring of scientific workflows, but usually depend on external development systems, with notations, which strive to support general workflows, but are still too complex for every-day use by biologists. The distinction between web-based and non-web based tools is likely to further irritate users. We extend our work on collaborative workflow design, by introducing a web-based scientific workflow system, that enables easy-to-use semantic service composition with a domain specific workflow notation.

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References

  1. 1.
    Taylor, I.J., Deelman, E., Gannon, D.B., Shields, M.: Workflows for e-Science: Scientific Workflows for Grids. Springer, New York (2006)Google Scholar
  2. 2.
    OASIS: Web Services Business Process Execution Language Version 2.0 (April 2007), http://docs.oasis-open.org/wsbpel/2.0/wsbpel-v2.0.pdf (last accessed October 24, 2007)
  3. 3.
    Held, M., Blochinger, W.: Structured collaborative workflow design. Future Generation Computer Systems 25(6), 638–653 (2009)CrossRefGoogle Scholar
  4. 4.
    Gil, Y., Deelman, E., Ellisman, M., Fahringer, T., Fox, G., Gannon, D., Goble, C., Livny, M., Moreau, L., Myers, J.: Examining the Challenges of Scientific Workflows. IEEE Computer 40(12), 24–32 (2007)Google Scholar
  5. 5.
    Barker, A., van Hemert, J.: Scientific Workflow: A Survey and Research Directions. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Wasniewski, J. (eds.) PPAM 2007. LNCS, vol. 4967, pp. 746–753. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  6. 6.
    Gibson, A., Gamble, M., Wolstencroft, K., Oinn, T., Goble, C.: The data playground: An intuitive workflow specification environment. In: E-SCIENCE 2007: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing, pp. 59–68. IEEE Computer Society, Washington (2007)CrossRefGoogle Scholar
  7. 7.
    Wilkinson, M.D., Links, M.: BioMOBY: an open-source biological web services proposal. Briefings In Bioinformatics 3(4), 331–341 (2002)CrossRefGoogle Scholar
  8. 8.
    The BioMoby Consortium: Interoperability with Moby 1.0 It’s better than sharing your toothbrush! Briefings In Bioinformatics 9(3) (2008)Google Scholar
  9. 9.
    Carrere, S., Gouzy, J.: REMORA: a pilot in the ocean of BioMoby web-services. Bioinformatics 22(7), 900–901 (2006)CrossRefGoogle Scholar
  10. 10.
    Bartocci, E., Corradini, F., Merelli, E., Scortichini, L.: BioWMS: a web-based Workflow Management System for bioinformatics. BMC Bioinformatics 8(1) (2007)Google Scholar
  11. 11.
    Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A., Li, P.: Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20(17), 3045–3054 (2004)CrossRefGoogle Scholar
  12. 12.
    Lanzén, A., Oinn, T.: The Taverna Interaction Service. Bioinformatics 24(8), 1118–1120 (2008)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Markus Held
    • 1
  • Wolfgang Blochinger
    • 2
  • Moritz Werning
    • 3
  1. 1.Symbolic Computation GroupEberhard Karls UniversityTübingenGermany
  2. 2.Institute of Parallel and Distributed SystemsUniversity of StuttgartStuttgartGermany
  3. 3.SUM IT AGBaden-DättwilSwitzerland

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