Translating SBML Models into the Stochastic π-Calculus for Stochastic Simulation

  • Claudio Eccher
  • Paola Lecca
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230)


This paper addresses the translation of Systems Biology Mark-Up Language (SBML) Level 2 models of network of biochemical reactions into the Biochemical Stochastic π-calculus (SPI). SBML is XML-based formalism for systems biology, while SPI can describe the concurrency of the different interactions occurring in a network of biochemical stochastic reactions. SPI models can be used for simulation by available computer packages. We present the approach followed in designing a software tool for working biologists that parses an SBML model and performs the unsupervised translation into the process algebra model. To test the correctness of the translation process we present the results obtained by performing simulations of a translated simplified circadian clock model, comparing our results with that obtained with the original differential equation model.


System Biology Order Reaction Process Algebra Second Order Reaction System Biology Markup Language 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Kitano, H.: Systems biology: a brief overview. Science 295, 1662–1664 (2002)CrossRefGoogle Scholar
  2. 2.
    Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.: Biopathways representation and simulation on hybrid functional petri net. Silico Biol. 3(3), 389–404 (2003)Google Scholar
  3. 3.
    Kam, N., Cohen, I., Harel, D.: The immune system as a reactive system: Modeling t cell activation with statecharts. In: Proc. Symposia on Human-Centric Computing Languages and Environments, pp. 15–22. IEEE Computer Society Press, Los Alamitos (2001)CrossRefGoogle Scholar
  4. 4.
    Kahn, S., Makkena, R., McGeary, F., Decker, K., Gillis, W., Schmidt, C.: A multi-agent system for the quantitative simulation of biological networks. In: Proceedings of the AAMAS 2003, Melbourne, Australia, pp. 385–392 (2003)Google Scholar
  5. 5.
    Peleg, M., Yeh, I., Altman, R.B.: Modeling biological processes using workflow and petri net models. Bioinformatics 18, 825–837 (2002)CrossRefGoogle Scholar
  6. 6.
    Winter, A., Kullbach, B., Riediger, V.: An overview of the GXL graph exchange language. In: Diehl, S. (ed.) Dagstuhl Seminar 2001. LNCS, vol. 2269, p. 324. Springer, Heidelberg (2002)CrossRefGoogle Scholar
  7. 7.
    The Bioinformatic Sequence Markup Language,
  8. 8.
    Finney, A., Hucka, M.: Systems biology markup language (sbml) level 2: Structures and facilities for model definitions, Available at:
  9. 9.
    Hucka, M., Finney, A., Bornstein, B.J., Keating, S.M., Shapiro, B.E., Matthews, J., Kovitz, B.L., Schilstra, M.J., Funahashi, A., Doyle, J.C., Kitano, H.: Evolving a lingua franca and associated software infrastructure for computational systems biology: The systems biology markup language (sbml) project. Systems Biology 1, 41–53 (2004)CrossRefGoogle Scholar
  10. 10.
    Kaneisha, M., Goto, S.: Kegg: Kyoto encyclopaedia of genes and genomes. Nucleic Acid Res. 28, 27–30 (2000)CrossRefGoogle Scholar
  11. 11.
    Priami, C., Regev, A., Shapiro, E., Silvermann, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information processing letters 80, 25–31 (2001)MATHCrossRefMathSciNetGoogle Scholar
  12. 12.
  13. 13.
    Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 123–152. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  14. 14.
    Lecca, P., Priami, C.: Cell cycle control in eukaryotes: a biospi model. Technical Report DIT-03-045, University of Trento (2003)Google Scholar
  15. 15.
    Regev, A., Silverman, W., Shapiro, B.E.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Proceedings of the Pacific Symposium of Biocomputing (PSB 2001), vol. 6, pp. 459–470 (2001)Google Scholar
  16. 16.
    Kuttler, C., Niehren, J., Blossey, R.: Gene regulation in the pi calculus: Simulating cooperativity at the lambda switch. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 24–55. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  17. 17.
    Lecca, P., Priami, C., Quaglia, P., Rossi, B., Laudanna, C., Costantin, G.: A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment. SIMULATION: Transactions of the society for modelling and simulation international 80, 273–288 (2004)CrossRefGoogle Scholar
  18. 18.
    The SBML BioModels Database,
  19. 19.
    Milner, R.: Communicating and Mobile Systems: the π-calculus. Cambridge University Press, Cambridge (1999)Google Scholar
  20. 20.
    Priami, C.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)CrossRefGoogle Scholar
  21. 21.
    Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340–2361 (1977)CrossRefGoogle Scholar
  22. 22.
    Blossey, R., Cardelli, L., Phillips, A.: A compositional approach to the stochastic dynamics of gene networks (2005), Available at:
  23. 23.
    Vilar, J.M.G., Kueh, H.Y., Barkai, N., Leibler, S.: Mechanisms of noise resistance in genetic oscillators. PNAS 99, 5992–5998 (2002)CrossRefGoogle Scholar
  24. 24.
    The Cellerator Web Site:
  25. 25.
    Shapiro, B.E., Mjolsness, E.D.: Developmental simulations with cellerator. In: Yi, T., Hucka, M., Morohashi, M., Kitano, H. (eds.) Proceedings of the Second International Conference on Systems Biology (ICSB 2001), Omnipress (2001)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Claudio Eccher
    • 1
    • 2
  • Paola Lecca
    • 1
  1. 1.Dept. of Information and Communication TechnologiesUniversity of TrentoItaly
  2. 2.ITC-irst Center for Scientific and Technological ResearchPovo (Trento)Italy

Personalised recommendations