Abstract
Process calculi hold great promise for modeling and analysis of cellular mechanics and behavior. While measured success has been achieved in their simulation of specific biochemical pathways and molecular mechanisms within the cell, several obstacles remain to their widespread adoption and use. Chiefly, these have to with the difficulty of modeling cell membranes and localized behavior, and limitations on the scalability of the execution model. This paper describes a multi-layered formalism – GridSPiM – that engages notions of concurrency, locality and encapsulation to provide a framework suitable for capturing the key aspects of cellular processes.
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
Abadi, M., Gordon, A.D.: A calculus for cryptographic protocols: The spi calculus. In: Fourth ACM Conference on Computer and Communications Security, pp. 36–47. ACM Press, New York (1997)
Armstrong, D.: Membrane traffic, from cell to clinic. In: Latchman, D. (ed.) Basic Molecular and Cell Biology, 3rd edn., pp. 116–126. BMJ Publishing Group, London (1997)
Blossey, R., Cardelli, L., Phillips, A.: Compositionality, stochasticity and cooperativity in dynamic models of gene regulation. HFSP Journal 2, 17–28 (2008)
Cardelli, L.: Brane calculi. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Cardelli, L., Gordon, A.: Mobile ambients. In: Nivat, M. (ed.) FOSSACS 1998. LNCS, vol. 1378, pp. 140–155. Springer, Heidelberg (1998)
Danos, V., Pradalier, S.: Projective brane calculus. In: Computational Methods in Systems Biology, pp. 134–148 (2004)
Gillespie, D.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Haugsten, E.M., Sorensen, V., Brech, A., Olsnes, S., Wesche, J.: Different intracellular trafficking of FGF1 endocytosed by the four homologous FGF receptors. Journal of Cell Science 118, 3869–3882 (2005)
Hoare, C.A.R.: Communicating sequential processes. Communications of the ACM 21, 666–677 (1978)
Milner, R.: A Calculus of Communication Systems. LNCS, vol. 92. Springer, Heidelberg (1980)
Milner, R.: A calculus of mobile processes (I and II). Information and Computation 100(1), 1–77 (1992)
Milner, R.: Communicating and mobile systems: the π-calculus. Cambridge University Press, Cambridge (1999)
Murtagh, L.J., Whiley, M., Wilson, S., Tran, H., Bassett, M.L.: Unsaturated iron binding capacity and transferrin saturation are equally reliable in detection of HFE hemochromatosis. American Journal of Gastroenterology 97, 2093–2099 (2002)
Phillips, A.: Efficient, correct abstract machines for stochastic process calculi with mobile compartments. Microsoft Research
Phillips, A., Cardelli, L.: A correct abstract machine for the stochastic pi-calculus. In: Transactions on Computational Systems Biology (2004)
Priami, C.: Stochastic π-calculus. The Computer Journal 38(6), 578–589 (1995)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic name passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Regev, A., Panina, E., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: an abstraction for biological compartments. Theoretical Computer Science, Special Issue on Computational Methods in Systems Biology 325(1), 141–167 (2004)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the pi-calculus process algebra. In: Proceedings of the Pacific Symposium of Biocomputing, vol. 6, pp. 459–470 (2001)
Singh, A.K., Coyne, D.W., Shapiro, W., Rizkala, A.R.: Predictors of the response to treatment in anemic hemodialysis patients with high serum ferritin and low transferrin saturation. Kidney International 71, 1163–1171 (2007)
Spector, A.A., Yorek, M.A.: Membrane lipid composition and cellular function. Journal of Lipid Research 26, 1015–1035 (1985)
Stathopoulos, A., Levine, M.: Dorsal gradient networks in the drosophila embryo. Developmental Biology 246, 57–67 (2002)
van Bakel, S., Kahn, I., Vigliotti, M.G., Heath, J.K.: Modelling intracellular fate of FGF receptors with bioambients. Electronic Notes in Theoretical Computer Science (2008)
Weng, G., Bhalla, U.S., Iyengar, R.: Complexity in biological signaling systems. Science 284, 92–96 (1999)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Tyree, S., Kuplicki, R., Sarratt, T., Fujan, S., Hale, J. (2009). GridSPiM: A Framework for Simple Locality and Containment in the Stochastic π-Calculus. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_38
Download citation
DOI: https://doi.org/10.1007/978-3-642-00727-9_38
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00726-2
Online ISBN: 978-3-642-00727-9
eBook Packages: Computer ScienceComputer Science (R0)