ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services

  • Patrick May
  • Hans-Christian Ehrlich
  • Thomas Steinke
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4128)


In life sciences, scientists are confronted with an exponential growth of biological data, especially in the genomics and proteomics area. The efficient management and use of these data, and its transformation into knowledge are basic requirements for biological research. Therefore, integration of diverse applications and data from geographically distributed computing resources will become a major issue. We will present the status of our efforts for the realization of an automated protein prediction pipeline as an example for a complex biological workflow scenario in a Grid environment based on Web services. This case study demonstrates the ability of an easy orchestration of complex biological workflows based on Web services as building blocks and Triana as workflow engine.


Structure Prediction Grid Environment Template Structure Protein Structure Prediction Slave Process 


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  1. 1.
    Baker, D., Sali, A.: Protein structure prediction and structural genomics. Science 294, 93–96 (2001)CrossRefGoogle Scholar
  2. 2.
    Moult, J.: A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol. 15, 285–289 (2005)CrossRefGoogle Scholar
  3. 3.
    Fischer, D., Barret, C., Bryson, K., Elofsson, A., Godzik, A., Jones, D., Karplus, K., Kelley, L., MacCallum, R., Pawowski, K., Rost, B., Rychlewski, L., Sternberg, M.: CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins 3, 209–217 (1999)CrossRefGoogle Scholar
  4. 4.
    Altschul, S.F., Madden, T.L., Schaffler, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nuc. Acids Res. 25, 3389–3402 (1997)CrossRefGoogle Scholar
  5. 5.
    Majithia, S., Shields, M., Taylor, I., Wang, I.: Triana: A graphical web service composition and execution toolkit. In: IEEE International Conference on Web Services (ICWS 2004) (2004)Google Scholar
  6. 6.
    Curbera, F., Andrews, T., Dholakia, H., Goland, Y., Klein, J., Leymann, F., Liu, K., Roller, D., Smith, D., Thatte, S., Trickovic, I., Weerawarana, S.: Business Process Execution Language for Web services, V.1.0 Available via, http://www-106.ibm.com/developerworks/webservices/library/ws-bpel
  7. 7.
    Leymann, F.: Web Service Flow Language WSFL, version 1.0Google Scholar
  8. 8.
    Triana Available via, http://www.trianacode.org
  9. 9.
    Gao, H.T., Hayes, J.H., Cai, H.: Integrating biological research through web services. Computer, 26–31 (2005)Google Scholar
  10. 10.
    Cavalcanti, M.C., Targino, R., Baião, F.A., Rössle, S.C., Bisch, P.M., Pires, P.F., Campos, M.L.M., Mattoso, M.: Managing structural genomic workflows using web services. Data Knowl. Eng. 53(1), 45–74 (2005)CrossRefGoogle Scholar
  11. 11.
    IBM BPWS4J, Available via, http://www.alphaworks.ibm.com/tech/bpws4j
  12. 12.
    Guo, J., Ellrott, K., Chung, W.J., Xu, D., Passovets, S., Xu, Y.: PROSPECT-PSPP: an automated computational pipeline for protein structure prediction. Nucleic Acid Res. (Web Server Issue) 32, W522–W525 (2004)CrossRefGoogle Scholar
  13. 13.
    Velankar, S., McNeil, P., Mittard-Runte, V., Suarez, A., Barrell, D., Apweiler, R., Henrick, K.: E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res. (Database issue)  33, D262–D265 (2005)CrossRefGoogle Scholar
  14. 14.
    Trissl, S., Rother, K., Muller, H., Steinke, T., Koch, I., Preissner, R., Froemmel, C., Leser, U.: Columba: an integrated database of proteins, structures, and annotations. BMC Bioinformatics 6(1), 81–92 (2005)CrossRefGoogle Scholar
  15. 15.
    HOBIT (Helmholtz Open Bioinformatics Technology) project Available via, http://hobit.sourceforge.net
  16. 16.
    Michalsky, E., Goede, A., Preissner, R., May, P., Steinke, T.: A distributed pipeline for structure prediction. In: CASP6 Methods Abstracts, 6th Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, pp. 112–114 (2004)Google Scholar
  17. 17.
    Berman, H., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T., Weissig, H., Shyndyalov, I., Bourne, P.: The protein data bank. Nucl. Acids Res 28, 235–242 (2000)CrossRefGoogle Scholar
  18. 18.
    Bairoch, A., Apweiler, R., Wu, C., Barker, W., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M., Natale, D., O’Donovan, C., Redaschi, N., Yeh, L.: The universal protein resource (uniprot). Nucleic Acids Res. 1(33), 154–159 (2005)Google Scholar
  19. 19.
    Marti-Renom, M., Stuart, A., Fiser, A., Sanchez, R., Melo, F., Sali, A.: Comparitive protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000)CrossRefGoogle Scholar
  20. 20.
    McGuffin, L., Bryson, K., Jones, D.: The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405 (2000)CrossRefGoogle Scholar
  21. 21.
    May, P., Steinke, T.: THESEUS - protein structure prediction at ZIB. ZIB Report 06-24 (2006)Google Scholar
  22. 22.
    Lathrop, R.H., Sazhin, A., Sun, Y., Steffen, N., Irani, S.S.: A multi-queue branch-and-bound algorithm for anytime optimal search with biological applications. Genome Informatics 12, 73–82 (2001)Google Scholar
  23. 23.
    BCB-Cluster Available via, http://elfie.bcbio.de
  24. 24.
    Apache Axis Available via, http://ws.apache.org/axis
  25. 25.
    Taylor, I., Wang, I., Shields, M., Majithia, S.: Distributed computing with triana on the grid. Concurrency and Computation:Practice and Experience 17, 1–18 (2005)CrossRefGoogle Scholar
  26. 26.
    MediGRID Available via, http://www.medigrid.de/

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Patrick May
    • 1
  • Hans-Christian Ehrlich
    • 1
  • Thomas Steinke
    • 1
  1. 1.Zuse Institute BerlinBerlinGermany

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