Advertisement

Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI

  • Anna-Lena Lamprecht
  • Tiziana Margaria
  • Bernhard Steffen
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

This paper shows how the agility provided by the Bio-jETI platform helps to interactively design bioinformatics analysis processes. Bio-jETI is a platform for the integration, orchestration and provision of services. The agility in design and execution is demonstrated by developing seven variations on a multiple sequence alignment workflow.

Keywords

Web services service orchestration model-driven development bioinformatics workflows 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Margaria, T., Kubczak, C., Steffen, B.: Bio-jETI: A Service Integration, Design, and Provisioning Platform for Orchestrated Bioinformatics Processes. BMC Bioinformatics (to appear) Google Scholar
  2. 2.
    Jörges, S., Kubczak, C., Nagel, R., Margaria, T., Steffen, B.: Model-Driven Development with the jABC. In: Bin, E., Ziv, A., Ur, S. (eds.) HVC 2006. LNCS, vol. 4383, Springer, Heidelberg (2007)Google Scholar
  3. 3.
    Margaria, T., Nagel, R., Steffen, B.: jETI: A Tool for Remote Tool Integration. In: Halbwachs, N., Zuck, L.D. (eds.) TACAS 2005. LNCS, vol. 3440, pp. 557–562. Springer, Heidelberg (2005)Google Scholar
  4. 4.
    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
  5. 5.
    Hull, D., Wolstencroft, K., Stevens, R., Goble, C.A., Pocock, M.R., Li, P., Oinn, T.: Taverna: A tool for building and running workflows of services. Nucleic Acids Research 34(Web-Server-Issue), 729–732 (2006)CrossRefGoogle Scholar
  6. 6.
    Altintas, I., Berkley, C., Jaeger, E., Jones, M., Ludäscher, B., Mock, S.: Kepler: An Extensible System for Design and Execution of Scientific Workflows. In: SSDBM, pp. 423–424 (2004)Google Scholar
  7. 7.
    Garvey, T.D., Lincoln, P., Pedersen, C.J., Martin, D., Johnson, M.: BioSPICE: Access to the Most Current Computational Tools for Biologists. OMICS - A Journal of Integrative Biology 7(4), 411–420 (2003)CrossRefGoogle Scholar
  8. 8.
    Majithia, S., Shields, M.S., Taylor, I.J., Wang, I.: Triana: A Graphical Web Service Composition and Execution Toolkit. In: Proceedings of the IEEE International Conference on Web Services (ICWS 2004), pp. 514–524. IEEE Computer Society, Los Alamitos (2004)CrossRefGoogle Scholar
  9. 9.
    Taylor, I., Shields, M., Wang, I., Harrison, A.: The Triana Workflow Environment: Architecture and Applications. In: Taylor, I., Deelman, E., Gannon, D., Shields, M. (eds.) Workflows for e-Science, Secaucus, NJ, USA, pp. 320–339. Springer, New York (2007)CrossRefGoogle Scholar
  10. 10.
    Deelman, E., Singh, G., Su, M.-H., Blythe, J., Gil, Y., Kesselman, C., Mehta, G., Vahi, K., Berriman, G.B., Good, J., Laity, A.C., Jacob, J.C., Katz, D.S.: Pgasus: A framework for mapping complex scientific workflows onto distributed systems. Scientific Programming 13(3), 219–237 (2005)Google Scholar
  11. 11.
    Chebotko, A., Lin, C., Fei, X., Lai, Z., Lu, S., Hua, J., Fotouhi, F.: View: A visual scientific workflow management system. In: IEEE SCW, pp. 207–208. IEEE Computer Society, Los Alamitos (2007)Google Scholar
  12. 12.
    Polanski, A.: Sequence Alignment. In: Bioinformatics, pp. 155–156. Springer, Heidelberg (2007)Google Scholar
  13. 13.
    Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673–4680 (1994)CrossRefGoogle Scholar
  14. 14.
    Hartmeier, S., Krüger, J., Giegerich, R.: Webservices and Workflows on the Bielefeld Bioinformatics Server: Practices and Problems. In: Proceedings of NETTAB 2007 Workshop: A Semantic Web for Bioinformatics (2007)Google Scholar
  15. 15.
    DDBJ: Web API for Bioinformatics (2007), http://xml.nig.ac.jp/wsdl/index.jsp
  16. 16.
    Pillai, S., Silventoinen, V., Kallio, K., Senger, M., Sobhany, S., Tate, J., Velankar, S., Golovin, A., Henrick, K., Rice, P., Stoehr, P., Lopez, R.: SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Research 33(1), 25 (2005)CrossRefGoogle Scholar
  17. 17.
    Labarga, A., Pilai, S., Valentin, F., Anderson, M., Lopez, R.: Web services at the European Bioinformatics Institute. EMBnet.news 11(4), 18–23 (2005)Google Scholar
  18. 18.
    Labarga, A., Valentin, F., Anderson, M., Lopez, R.: Web Services at the European Bioinformatics Institute. Nucleic Acids Research Web Server Issue (2007)Google Scholar
  19. 19.
    Zmasek, C.M., Eddy, S.R.: ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17(4), 383–384 (2001)CrossRefGoogle Scholar
  20. 20.
    Lamprecht, A.-L., Margaria, T., Steffen, B.: GeneFisher-P: Variations of GeneFisher as Processes in Bio-jETI. In: Proceedings of NETTAB 2007 Workshop: A Semantic Web for Bioinformatics (2007)Google Scholar
  21. 21.
    Seibel, P.N., Krüger, J., Hartmeier, S., Schwarzer, K., Löwenthal, K., Mersch, H., Dandekar, T., Giegerich, R.: XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinformatics 7, 490 (2006)CrossRefGoogle Scholar
  22. 22.
    BioJava Project: Main Page - BioJava, http://biojava.org
  23. 23.
    Lamprecht, A.-L., Margaria, T., Steffen, B., Sczyrba, A., Hartmeier, S., Giegerich, R.: GeneFisher-P: Variations of GeneFisher as Processes in BiojETI. BMC Bioinformatics (to appear)Google Scholar
  24. 24.
    Margaria, T., Kubczak, C., Njoku, M., Steffen, B.: Model-Based Design of Distributed Collaborative Bioinformatics Processes in the jABC. In: Proc. ICECCS 2006, IEEE International Conference on Engineering of Complex Computer Systems (August 2006)Google Scholar
  25. 25.
    Kubczak, C., Margaria, T., Fritsch, A., Steffen, B.: Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms. In: Proceedings of the 2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (ISoLA 2006), Paphos, Cyprus, pp. 308–313. IEEE Computer Society Press, Los Alamitos (2006)Google Scholar
  26. 26.
    Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13, 2498–2504 (2003)CrossRefGoogle Scholar
  27. 27.
    Margaria, T., Steffen, B.: Ltl guided planning: Revisiting automatic tool composition in eti. In: SEW, pp. 214–226. IEEE Computer Society, Los Alamitos (2007)Google Scholar
  28. 28.
    SWS Challenge: Challenge on Automating Web Services Mediation, Choreography and Discovery, http://sws-challenge.org/

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Anna-Lena Lamprecht
    • 1
    • 2
  • Tiziana Margaria
    • 3
  • Bernhard Steffen
    • 1
  1. 1.Chair of Programming SystemsDortmund University of TechnologyDortmundGermany
  2. 2.Center of Applied ProteomicsDortmundGermany
  3. 3.Chair of Service and Software EngineeringPotsdam UniversityPotsdamGermany

Personalised recommendations