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DynamicFlow: A Client-Side Workflow Management System

  • Pedro Lopes
  • Joel Arrais
  • José Luís Oliveira
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5518)

Abstract

The constant increase on the amount and heterogeneity of biological data sources impose a permanent pressure toward the development of computational solutions that can integrate and process all the data, and help give answers to arising biological questions. Besides the work already developed on information integration in computational biology, the novel Web2.0 and Web Semantic trends leverage the design of next-generation applications sustained by the web-as-a-platform principle. Grounded on this idea, this paper presents a service orchestration framework that, using existing web components, allows the user to create and execute their own research workflow relying simply on a normal web browser.

Keywords

service orchestration workflow web service data integration Web2.0 

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References

  1. 1.
    Watson, J.D.: The human genome project: past, present, and future. Science 248, 44–49 (1990)CrossRefGoogle Scholar
  2. 2.
    Cheung, K.-H., Yip, K.Y., Townsend, J.P., Scotch, M.: HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0. Journal of Biomedical Informatics 41, 694–705 (2008)CrossRefGoogle Scholar
  3. 3.
    de Knikker, R., Guo, Y., Li, J.-l., Kwan, A., Yip, K., Cheung, D., Cheung, K.-H.: A web services choreography scenario for interoperating bioinformatics applications. BMC Bioinformatics 5, 25 (2004)CrossRefGoogle Scholar
  4. 4.
    Margaria, T., Kubczak, C., Steffen, B.: Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes. BMC Bioinformatics 9, S12 (2008)CrossRefGoogle Scholar
  5. 5.
    Goble, C., Stevens, R.: State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics 41, 687–693 (2008)CrossRefGoogle Scholar
  6. 6.
    Ludascher, B., Altintas, I., Berkley, C., Higgings, D., Jaeger, E., Jones, M., Lee, E.A., Tao, J., Zhao, Y.: Taverna: Scientific Workflow Management and the Kepler System. Research Articles, Concurrency and Computation: Practice & Experience 18, 1039–1065 (2006)CrossRefGoogle Scholar
  7. 7.
    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, 3045–3054 (2004)CrossRefGoogle Scholar
  8. 8.
    Romano, P., Marra, D., Milanesi, L.: Web services and workflow management for biological resources. BMC Bioinformatics 6, S24 (2005)CrossRefGoogle Scholar
  9. 9.
    Guan, Z., Jamil, H.M.: Streamlining biological data analysis using BioFlow. In: Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings, pp. 258–262 (2003)Google Scholar
  10. 10.
    Wilkinson, M., Links, M.: BioMoby: An open source biological web services proposal. Brief. Bioinform. 3, 331–341 (2002)CrossRefGoogle Scholar
  11. 11.
    Carole Anne, G., David Charles De, R.: myExperiment: social networking for workflow-using e-scientists. In: Proceedings of the 2nd workshop on Workflows in support of large-scale science. ACM, Monterey (2007)Google Scholar
  12. 12.
    Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Sci. Am. 284, 34–43 (2001)CrossRefGoogle Scholar
  13. 13.
    Fielding, R.: Semantic Web Services Challenge: Architectural Styles and the Design of Network-based Software Architectures. In: Semantic Web Services Challenge: Challenge on Automating Web Services Mediation, Choreography and Discovery: 2006, Stanford University, USA (2000)Google Scholar
  14. 14.
    Cannata, N., Schroder, M., Marangoni, R., Romano, P.: A Semantic Web for bioinformatics: goals, tools, systems, applications. BMC Bioinformatics 9, S1 (2008)CrossRefGoogle Scholar
  15. 15.
    Belleau, F., Nolin, M.-A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics 41, 706–716 (2008)CrossRefGoogle Scholar
  16. 16.
    Splendiani, A.: RDFScape: Semantic Web meets Systems Biology. BMC Bioinformatics 9, S6 (2008)CrossRefGoogle Scholar
  17. 17.
    Zhao, Q., Huang, G., Huang, J., Liu, X., Mei, H.: A Web-Based Mashup Environment for On-the-Fly Service Composition. In: IEEE International Symposium on Service-Oriented System Engineering, 2008. SOSE 2008, pp. 32–37 (2008)Google Scholar
  18. 18.
    Cardoso, J., Sheth, A.: Semantic E-Workflow Composition. Journal of Intelligent Information Systems (2003)Google Scholar
  19. 19.
    Stein, L.D.: Integrating biological databases. Nat. Rev. Genet. 4, 337–345 (2003)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Pedro Lopes
    • 1
  • Joel Arrais
    • 1
  • José Luís Oliveira
    • 1
  1. 1.IEETA, Universidade de AveiroAveiroPortugal

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