Advertisement

A Stochastic Semantics for BioAmbients

  • Linda Brodo
  • Pierpaolo Degano
  • Corrado Priami
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4671)

Abstract

We consider BioAmbients, a calculus for specifying biological entities and for simulating and analysing their behaviour. We extend BioAmbients to take quantitative information into account by defining a stochastic semantics, based on a simulation stochastic algorithm, to determine the actual rate of transitions.

Keywords

Process Calculi Stochastic Operational Semantics Systems Biology 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An abstraction for biological compartments. Th. Comp. Sci. 325(1), 141–167 (2004)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Calder, M., Gilmore, S., Hillston, J.: Modelling the influence of RKIP an the ERK signalling pathway using the stochastic process algebra PEPA. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Nielson, H.R. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol. 4230, pp. 1–23. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  3. 3.
    Calzone, L., Chabrier-River, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, p. 68. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  4. 4.
    Cardelli, L.: Brane calculi - interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–280. Springer, Heidelberg (2005)Google Scholar
  5. 5.
    Cardelli, L., Gordon, A.: Mobile ambients. Th. Comp. Sci. 240(1), 177–213 (2000)zbMATHCrossRefMathSciNetGoogle Scholar
  6. 6.
    Cardelli, L., Philips, A.: A correct abstract machine for the stochastic π-calculus. In: Proc. Concurrent Models in Molecular Biology (2004)Google Scholar
  7. 7.
    Chiarugi, D., Curti, M., Degano, P., Lo Brutto, G., Marangoni, R.: Feedbacks and oscillations in the virtual cell VICE. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, p. 93. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  8. 8.
    Clark, G., Hillston, J.: Towards automatic derivation of performance measures from pepa models. In: Proc. UK Performance Engineering Workshop, pp. 65–81 (1996)Google Scholar
  9. 9.
    Danos, V., Laneve, C.: Formal molecular biology. Th. Comp. Sci. 325(1), 69–110 (2004)zbMATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    Goss, P., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology by using stochastic petri nets. Proc. National Academy of Science USA 95, 6750–6754 (1998)CrossRefGoogle Scholar
  11. 11.
    Heat, J., Kwiatkowska, M., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol. 4210, p. 32. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  12. 12.
    Hoare, C.: Communicating Sequential Processes. Prentice-Hall, Englewood Cliffs (1985)zbMATHGoogle Scholar
  13. 13.
    Kitano, H.: Foundations of Systems Biology. MIT Press, Cambridge (2002)Google Scholar
  14. 14.
    Lecca, P., Priami, C., Quaglia, P., Rossi, B., Laudanna, C., Costantin, G.: A stochastic process algebra approach to simulation of autoreactive lymphocyte recruiment. SIMULATION 80(4) (2004)Google Scholar
  15. 15.
    Milner, R.: Communication and Concurrency. Prentice-Hall, Englewood Cliffs (1989)zbMATHGoogle Scholar
  16. 16.
    Milner, R., Parrow, J., Walker, D.: A calculus of mobile processes (i and ii). Information and Computation 100(1), 1–72 (1992)zbMATHCrossRefMathSciNetGoogle Scholar
  17. 17.
    Nagasaki, M., Onami, S., Miyano, S., Kitano, H.: Bio-calculus: Its concept and an application for molecular interaction. Frontiers Science Series 30 (2000)Google Scholar
  18. 18.
    Priami, C.: Stochastic π-calculus. The Computer Journal 38(7), 578–589 (1995)CrossRefGoogle Scholar
  19. 19.
    Priami, C., Quaglia, P.: Beta-binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 21–34. Springer, Heidelberg (2005)Google Scholar
  20. 20.
    Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80(1), 25–31 (2001)zbMATHCrossRefMathSciNetGoogle Scholar
  21. 21.
    Regev, A.: Computational Systems Biology: A Calculus for Biomolecular knowledge. PhD thesis, Tel Aviv University (2002)Google Scholar
  22. 22.
    Regev, A., Shapiro, E.T., Silverman, W.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Proc. Pacific Symposium on Biocomputing, vol. 6, pp. 459–470 (2001)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Linda Brodo
    • 1
  • Pierpaolo Degano
    • 2
  • Corrado Priami
    • 3
  1. 1.Dipartimento di Scienze dei Linguaggi - via Tempio 9, I-07100 SassariItalia
  2. 2.Dipartimento di Informatica - Largo Pontecorvo 3, I-56127 PisaItalia
  3. 3.The Microsoft Research - University of Trento Centre for Computational and Systems Biology - Piazza Manci 17, I-38100 Povo (Tn)Italia

Personalised recommendations