Abstract
Programming language technology can contribute to the development and understanding of Systems Biology by providing formal calculi for specifying and analysing the dynamic behaviour of biological systems. Our focus is on BioAmbients, a variation of the ambient calculi developed for modelling mobility in computer systems. We present a static analysis for capturing the spatial structure of biological systems and we illustrate it on a few examples.
This research has been supported by the LoST project (number 21-02-0507) funded the Danish Natural Science Research Council.
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.
Similar content being viewed by others
References
Bugliesi, M., Castagna, G., Crafa, S.: Boxed Ambients. In: Kobayashi, N., Pierce, B.C. (eds.) TACS 2001. LNCS, vol. 2215, pp. 37–63. Springer, Heidelberg (2001)
Cardelli, L.: Brane calculi (2003), Available from http://www.luca.demon.co.uk
Cardelli, L., Gordon, A.D.: Mobile Ambients. In: Nivat, M. (ed.) FOSSACS 1998. LNCS, vol. 1378, pp. 140–155. Springer, Heidelberg (1998)
Bodei, C., Degano, P., Priami, C., Zannone, N.: An enhanced cfa for security policies. In: Proceedings of the Workshop on Issues on the Theory of Security (WITS 2003) (co-located with ETAPS 2003) (2003)
Danos, V., Laneve, C.: Core formal molecular biology. In: Degano, P. (ed.) ESOP 2003. LNCS, vol. 2618, pp. 302–318. Springer, Heidelberg (2003)
Levi, F., Sangiorgi, D.: Controlling interference in ambients. In: Proceedings of the 27th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages (POPL 2000), pp. 352–364. ACM Press, New York (2000)
Milner, R.: Communicating and Mobile Systems: The pi-Calculus. Cambridge University Press, Cambridge (1999)
Nagasaki, M., Onami, S., Miyano, S.: Kitano H. Bio-calculus: Its concept and molecular interaction. Genome Informatics 10, 133–143 (1999)
Nielson, F., Riis Nielson, H., Priami, C., Schuch da Rosa, D.: Control Flow Analysis for BioAmbients. In: Proceedings of BioConcur., to appear in ENTCS (2004)
Nielson, F., Riis Nielson, H., Seidl, H.: A succinct solver for ALFP. Nordic Journal of Computing 9, 335–372 (2002)
Nielson, H.R., Nielson, F., Buchholtz, M.: Security for Mobility. In: Focardi, R., Gorrieri, R. (eds.) FOSAD 2001. LNCS, vol. 2946, pp. 207–265. Springer, Heidelberg (2004)
Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic passing-name calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25–31 (2001)
Regev, A.: Computational system biology: A calculus for biomolecular knowledge. PhD thesis, Tel Aviv University (2003)
Regev, A., Panina, E.M., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: An abstraction for biological compartments. Theoretical Computer Science (2004) (to appear)
Regev, A., Silverman, W., Shapiro, E.: Representation and simulation of biochemical processes using the π-calculus process algebra. In: Pacific Symposium of Biocomputing (PSB 2001), pp. 459–470 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2004 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Nielson, H.R., Nielson, F., Pilegaard, H. (2004). Spatial Analysis of BioAmbients. In: Giacobazzi, R. (eds) Static Analysis. SAS 2004. Lecture Notes in Computer Science, vol 3148. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-27864-1_8
Download citation
DOI: https://doi.org/10.1007/978-3-540-27864-1_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22791-5
Online ISBN: 978-3-540-27864-1
eBook Packages: Springer Book Archive