Nothing Special   »   [go: up one dir, main page]
Skip to main content
Springer Nature Link
Log in

The Attributed Pi Calculus

  • Conference paper
Computational Methods in Systems Biology (CMSB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5307))

Included in the following conference series:

Abstract

The attributed pi calculus \(({\phi({\mathcal L})})\) forms an extension of the pi calculus with attributed processes and attribute dependent synchronization. To ensure flexibility, the calculus is parametrized with the language \({\mathcal L}\) which defines possible values of attributes. \({\phi({\mathcal L})}\) can express polyadic synchronization as in pi@ and thus diverse compartment organizations. A non-deterministic and a stochastic semantics, where rates may depend on attribute values, is introduced. The stochastic semantics is based on continuous time Markov chains. A simulation algorithm is developed which is firmly rooted in this stochastic semantics. Two examples underline the applicability of \({\phi({\mathcal L})}\) to systems biology: Euglena’s movement in phototaxis, and cooperative protein binding in gene regulation of bacteriophage lambda.

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. Regev, A., Shapiro, E.: Cells as Computation. Nature 419, 343 (2002)

    Article  CAS  PubMed  Google Scholar 

  2. Regev, A.: Computational Systems Biology: A Calculus for Biomolecular Knowledge. Tel Aviv University, PhD thesis (2003)

    Google Scholar 

  3. 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, 25–31 (2001)

    Article  Google Scholar 

  4. Phillips, A., Cardelli, L.: Efficient, Correct Simulation of Biological Processes in the Stochastic Pi Calculus. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 184–199. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  5. Kuttler, C., Lhoussaine, C., Niehren, J.: A Stochastic Pi Calculus for Concurrent Objects. In: Anai, H., Horimoto, K., Kutsia, T. (eds.) Ab 2007. LNCS, vol. 4545, pp. 232–246. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  6. Dematté, L., Priami, C., Romanel, A.: Modelling and Simulation of Biological Processes in BlenX. SIGMETRICS Performance Evaluation Review 35(4), 32–39 (2008)

    Article  Google Scholar 

  7. Ciocchetta, F., Hillston, J.: Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks. ENTCS 194(3), 103–117 (2008)

    Google Scholar 

  8. Chabrier-Rivier, N., Fages, F., Soliman, S.: The Biochemical Abstract Machine BIOCHAM. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 172–191. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  9. Faeder, J.R., Blinov, M.L., Goldstein, B., Hlavacek, W.S.: Rule-Based Modeling of Biochemical Networks. Complexity 10(4), 22–41 (2005)

    Article  Google Scholar 

  10. Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling of cellular signalling. In: Caires, L., Vasconcelos, V.T. (eds.) CONCUR 2007. LNCS, vol. 4703, pp. 17–41. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  11. Hillston, J.: Process Algebras for Quantitative Analysis. In: LICS 2005: Proceedings of the 20th Annual IEEE Symposium on Logic in Computer Science, pp. 239–248. IEEE Computer Society, Los Alamitos (2005)

    Google Scholar 

  12. Cardelli, L.: On Process Rate Semantics. TCS 391(3), 190–215 (2008)

    Article  Google Scholar 

  13. Jaffar, J., Lassez, J.L.: Constraint Logic Programming. In: 14th ACM SIGACT-SIGPLAN Symposium on Principles of Programming Languages, pp. 111–119. ACM Press, New York (1987)

    Chapter  Google Scholar 

  14. Saraswat, V.A., Rinard, M., Panangaden, P.: The Semantic Foundations of Concurrent Constraint Programming. In: 18th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, pp. 333–352. ACM Press, New York (1991)

    Chapter  Google Scholar 

  15. Versari, C.: A Core Calculus for a Comparative Analysis of Bio-inspired Calculi. Programming Languages and Systems, pp. 411–425 (2007)

    Google Scholar 

  16. Kuttler, C.: Modeling Bacterial Gene Expression in a Stochastic Pi Calculus with Concurrent Objects. PhD thesis, Université des Sciences et Technologies de Lille - Lille 1 (2007)

    Google Scholar 

  17. Kuttler, C., Niehren, J.: Gene regulation in the pi calculus: Simulating cooperativity at the lambda switch. Transactions on Computational Systems Biology VII, 24–55 (2006)

    Google Scholar 

  18. Versari, C., Busi, N.: Stochastic Simulation of Biological Systems with Dynamical Compartment Structure. In: Calder, M., Gilmore, S. (eds.) CMSB 2007. LNCS (LNBI), vol. 4695, pp. 80–95. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  19. Versari, C., Busi, N.: Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes. ENTCS 194(3), 165–180 (2008)

    Google Scholar 

  20. Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An Abstraction for Biological Compartments. TCS 325(1), 141–167 (2004)

    Article  Google Scholar 

  21. Cardelli, L.: Brane calculi. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  22. John, M., Ewald, R., Uhrmacher, A.M.: A Spatial Extension to the Pi Calculus. ENTCS 194(3), 133–148 (2008)

    Google Scholar 

  23. Kholodenko, B.N.: Cell-Signalling Dynamics in Time and Space. Nature Reviews Molecular Cell Biology 7(3), 165–176 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Grell, K.G.: Protozoologie. Springer, Heidelberg (1968)

    Book  Google Scholar 

  25. Gillespie, D.T.: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. Journal of Computational Physics 22(4), 403–434 (1976)

    Article  CAS  Google Scholar 

  26. Khomenko, V., Meyer, R.: Checking Pi Calculus Structural Congruence is Graph Isomorphism Complete. Technical Report CS-TR: 1100, School of Computing Science, Newcastle University, 20 pages (2008)

    Google Scholar 

  27. Cappello, I., Quaglia, P.: A translation of beta-binders in a prioritized pi-calculus. In: From Biology to Concurrency and back, Workshop FBTC (2008)

    Google Scholar 

  28. Ewald, R., Jeschke, M.: Large-Scale Design Space Exploration of SSA. In: Computational Methods in Systems Biology, International Conference CMSB 2008. LNCS. Springer, Heidelberg (2008)

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. University of Rostock, Institute of Computer Science, Modeling and Simulation Group, Germany

    Mathias John & Adelinde M. Uhrmacher

  2. University of Lille 1, LIFL, CNRS UMR8022, France

    Cédric Lhoussaine

  3. INRIA, Lille, Mostrare project, France

    Joachim Niehren

  4. BioComputing project, LIFL, Lille, France

    Cédric Lhoussaine & Joachim Niehren

Authors
  1. Mathias John
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Cédric Lhoussaine
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joachim Niehren
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Adelinde M. Uhrmacher
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Computer Science, Brandenburg University of Technology, Postbox 10 13 44, 03013, Cottbus, Germany

    Monika Heiner

  2. University of Rostock, Albert-Einstein-Str. 21, D-18059, Rostock, Germany

    Adelinde M. Uhrmacher

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

John, M., Lhoussaine, C., Niehren, J., Uhrmacher, A.M. (2008). The Attributed Pi Calculus. In: Heiner, M., Uhrmacher, A.M. (eds) Computational Methods in Systems Biology. CMSB 2008. Lecture Notes in Computer Science(), vol 5307. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88562-7_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-88562-7_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88561-0

  • Online ISBN: 978-3-540-88562-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation