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
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Regev, A., Shapiro, E.: Cells as Computation. Nature 419, 343 (2002)
Regev, A.: Computational Systems Biology: A Calculus for Biomolecular Knowledge. Tel Aviv University, PhD thesis (2003)
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)
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)
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)
Dematté, L., Priami, C., Romanel, A.: Modelling and Simulation of Biological Processes in BlenX. SIGMETRICS Performance Evaluation Review 35(4), 32–39 (2008)
Ciocchetta, F., Hillston, J.: Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks. ENTCS 194(3), 103–117 (2008)
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)
Faeder, J.R., Blinov, M.L., Goldstein, B., Hlavacek, W.S.: Rule-Based Modeling of Biochemical Networks. Complexity 10(4), 22–41 (2005)
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)
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)
Cardelli, L.: On Process Rate Semantics. TCS 391(3), 190–215 (2008)
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)
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)
Versari, C.: A Core Calculus for a Comparative Analysis of Bio-inspired Calculi. Programming Languages and Systems, pp. 411–425 (2007)
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)
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)
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)
Versari, C., Busi, N.: Efficient Stochastic Simulation of Biological Systems with Multiple Variable Volumes. ENTCS 194(3), 165–180 (2008)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An Abstraction for Biological Compartments. TCS 325(1), 141–167 (2004)
Cardelli, L.: Brane calculi. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
John, M., Ewald, R., Uhrmacher, A.M.: A Spatial Extension to the Pi Calculus. ENTCS 194(3), 133–148 (2008)
Kholodenko, B.N.: Cell-Signalling Dynamics in Time and Space. Nature Reviews Molecular Cell Biology 7(3), 165–176 (2006)
Grell, K.G.: Protozoologie. Springer, Heidelberg (1968)
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)
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)
Cappello, I., Quaglia, P.: A translation of beta-binders in a prioritized pi-calculus. In: From Biology to Concurrency and back, Workshop FBTC (2008)
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)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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)