Skip to main content
Springer Nature Link
Log in

Design and Architecture of Web Services for Simulation of Biochemical Systems

  • Conference paper
Data Integration in the Life Sciences (DILS 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5647))

Included in the following conference series:

  • 530 Accesses

Abstract

Computer simulation of biochemical networks plays a central role in systems biology. While there are several software packages for modeling and simulation of these networks, they are based on graphical user interfaces that operate on the local computer. However, it is now often desirable to operate simulation tasks through a distributed computing framework where data can be gathered from different sources and distinct subtasks operated in different physical computers. In this paper we describe a web services implementation for the COPASI biochemical network simulator (CopasiWS). COPASI provides a range of numerical methods for simulation, optimization and analysis of biochemical reaction networks. Our aim is to allow easy integration of these powerful functionalities with local and remote services to provide a distributed computing platform for the simulation and analysis of biochemical models. One immediate result of this work is that simulation tasks are now available to be used in a platform– and language–independent manner as components of distributed workflows, for example using the Taverna workflow engine. We describe the CopasiWS architecture, key design and implementation issues, and illustrate the range of services available through a web portal interface (CopasiWeb).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., Kummer, U.: COPASI — a COmplex PAthway SImulator. Bioinformatics 22, 3067–3074 (2006)

    Article  CAS  PubMed  Google Scholar 

  2. Funahashi, A., Tanimura, N., Morohashi, M., Kitano, H.: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1, 159–162 (2003)

    Article  Google Scholar 

  3. Sauro, H.M., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., Kitano, H.: Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration. A Journal of Integrative Biology 7(4), 355–372 (2003)

    Article  CAS  PubMed  Google Scholar 

  4. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M.: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 27(1), 29–34 (1999)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Baxevanis, A.D.: Searching NCBI databases using Entrez. Current protocols in bioinformatics 24, 1.3.1–1.3.26 (2008)

    Google Scholar 

  6. Labarga, A., Valentin, F., Anderson, M., Lopez, R.: Web services at the European bioinformatics institute. Nucleic Acids Research 35, W6–W11 (2007)

    Article  Google Scholar 

  7. Le Novére, N., Bornstein, B., Broicher, A., Courtot, M., Donizell, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J., Hucka, M.: Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34, D689–D691 (2006)

    Article  Google Scholar 

  8. Le Novére, N., Finney, A., Hucka, M., Bhalla, U.S., Campagne, F., Collado-Vides, J., Crampin, E.J., Halstead, M., Klipp, E., Mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J., Spence, H., Wanner, B.: Minimum Information Requested In the Annotation of Biochemical Models (MIRIAM). Nature Biotechnology 23(12), 1509–1515 (2005)

    Article  PubMed  Google Scholar 

  9. Systems Biology Ontology (SBO), http://www.ebi.ac.uk/sbo/

  10. Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M.R., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nucleic Acids Research, W729–W732 (2006)

    Google Scholar 

  11. Taylor, I., Shields, M., Wang, I., Harrison, A.: The Triana Workflow Environment: Architecture and Application. In: Taylor, I.J., Deelman, E., Gannon, D.B., Shields, M. (eds.) Workflows for e-Science. Scientific Workflows for Grids, pp. 320–339. Springer, London (2007)

    Google Scholar 

  12. Mendes, P.: GEPASI: A software package for modeling the dynamics, steady states and control of biochemical biology and other systems. Computer Application in the Biosciences 9(5), 563–571 (1993)

    CAS  Google Scholar 

  13. Hucka, M., Finney, A., Sauro, H.M., Bolouri, H., Doyle, J.C., Kitano, H., Arkin, A.P., Bornstein, B.J., Bray, D., Cornish-Bowden, A., Cuellar, A.A., Dronov, S., Gilles, E.D., Ginkel, M., Gor, V., Goryanin, I., Hedley, W.J., Hodgman, T.C., Hofmeyr, J.H., Hunter, P.J., Juty, N.S., Kasberger, J.L., Kremling, A., Kummer, U., Le Novére, N., Loew, L.M., Lucio, D., Mendes, P., Minch, E., Mjolsness, E.D., Nakayama, Y., Nelson, M.R., Nielsen, P.F., Sakurada, T., Schaff, J.C., Shapiro, B.E., Shimizu, T.S., Spence, H.D., Stelling, J., Takahashi, K., Tomita, M., Wagner, J., Wang, J.: The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)

    Article  CAS  PubMed  Google Scholar 

  14. Web Services Interoperability Basic Profile, 1.1, http://www.ws-i.org/Profiles/BasicProfile-1.1.html

  15. Bornstein, B.J., Keating, S.M., Jouraku, A., Hucka, M.: LibSBML: An API Library for SBML. Bioinformatics 24(6), 880–881 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Dada, J.O., Paton, N.W., Mendes, P.: Systems Biology Results Markup Language — Structure and Facilities for Systems Biology Results Representation (SBRML Specification) (2008), http://www.comp-sys-bio.org/tiki-index.php?page=SBRML

  17. Thain, D., Tannenbaum, T., Livny, M.: Distributed Computing in Practice: The Condor Experience. Concurrency and Computation: Practice and Experience 17, 2–4 (2005)

    Article  Google Scholar 

  18. Petzold, L.: Automatic selection of methods for solving stiff and nonstiff systems of ordinary differential equations. SIAM Journal on Scientific and Statistical Computing 4(1), 136–148 (1983)

    Article  Google Scholar 

  19. Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25), 2340–2361 (1977)

    Article  CAS  Google Scholar 

  20. Fell, D.: Understanding the Control of Metabolism. Portland Press, London (1996)

    Google Scholar 

  21. Mendes, P., Kell, D.: Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14(10), 869–883 (1998)

    Article  CAS  PubMed  Google Scholar 

  22. Java programming language, http://java.sun.com

  23. Axis toolkit site, http://ws.apache.org/axis/

  24. Tomcat Apache servlet site, http://tomcat.apache.org/

  25. Copasi Web Services Services, http://turing.mib.man.ac.uk:8080/CopasiWS/services/listServices

  26. Apache Struts 2, http://struts.apache.org/2.x/

  27. CopasiWeb: Web Portal Interface to CopasiWS, http://turing.mib.man.ac.uk:8080/CopasiWeb/CopasiWebUI/

  28. Li, P., Oinn, T., Soiland, S., Kell, D.B.: Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics 24(2), 287–289 (2008)

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Computer Science and Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester, M1 7DN, UK

    Joseph O. Dada & Pedro Mendes

  2. Virginia Bioinformatics Institute, Virginia Tech, Washington Street 0477, Blacksburg, VA, 24060, USA

    Pedro Mendes

Authors
  1. Joseph O. Dada
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pedro Mendes
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Computer Science, University of Manchester, M13 9PL, Manchester, UK

    Norman W. Paton  & Paolo Missier  & 

  2. School of Computer Science, The University of Manchester, Oxford Road, M13 9PL, Manchester, UK

    Cornelia Hedeler

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Dada, J.O., Mendes, P. (2009). Design and Architecture of Web Services for Simulation of Biochemical Systems. In: Paton, N.W., Missier, P., Hedeler, C. (eds) Data Integration in the Life Sciences. DILS 2009. Lecture Notes in Computer Science(), vol 5647. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02879-3_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-02879-3_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02878-6

  • Online ISBN: 978-3-642-02879-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics