Abstract
We model qualitative and quantitative aspects of metabolic pathways by using a stochastic version of Multiset Rewriting (SMSR). They offer a natural way of describing both the static and the dynamic aspects of metabolic pathways. We argue that, due to its simple conceptual model, SMSR may be conveniently used as an intermediate language where many higher level specification languages may be compiled (e.g., as in the security protocol example). As a first step, we show also how SMSR may be used to simulate Stochastic Petri Nets for describing metabolic pathways.
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
Pevzner, A.: Computational Molecular Biology. MIT Press, Cambridge (2000)
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 (2001)
Cervesato, I., Durgin, N., Lincoln, P.D., Mitchell, J.C., Scedrov, A.: A Meta- Notation for Protocol Analysis. In: 12th Computer Security Foundations Workshop – CSFW-12, Mordano, Italy, pp. 55–69. IEEE Computer Society Press, Los Alamitos (1999)
Cervesato, I.: A Specification Language for Crypto-Protocols based on Multiset Rewriting, Dependent Types and Subsorting. In: Delzanno, G., Etalle, S., Gabbrielli, M. (eds.) Workshop on Specification, Analysis and Validation for Emerging Technologies – SAVE 2001, Paphos, Cyprus, pp. 1–22 (2001)
Gillespie, D.: Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81, 2340–2361 (1977)
Goss, P., Peccoud, J.: Quantitatice modeling of stochastic systems in molecular biology by using stochastic Petri Nets. In: Proc. National Academy of Sciences USA, vol. 95, pp. 6750–6754 (1998)
Bistarelli, S., Cervesato, I., Lenzini, G., Martinelli, F.: Relating process algebras and multiset rewriting (for example for security protocol analysis). Technical report, Istituto di Scienza e Tecnologie dell’Informazione (ISTI-CNR) (2002) (to appear)
Denker, G., Millen, J.K.: CAPSL Intermediate Language. In: Heintze, N., Clarke, E. (eds.) Proceedings of the Workshop on Formal Methods and Security Protocols – FMSP, Trento, Italy (1999)
Eker, S., Knapp, M., Laderoute, K., Lincoln, P., Meseguer, J., Sonmez, K.: Pathway logic: Symbolic analysis of biological signaling. In: Proc. Pacific Symposium on Biocomputing, vol. 7, pp. 400–412 (2002)
Hofestädt, R., M.L.u.U.S.: Molecular information fusion for metabolic networks. In: Xue, G.X., Xue, Y.B., Xu, Z.H., Holmes, R., Hammond, G., Lim, H.A. (eds.) Herausgeber, Gene Families: Studies of DNA, RNA, Enzymes and Proteins, pp. 221–232 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bistarelli, S., Cervesato, I., Lenzini, G., Marangoni, R., Martinelli, F. (2003). On Representing Biological Systems through Multiset Rewriting. In: Moreno-Díaz, R., Pichler, F. (eds) Computer Aided Systems Theory - EUROCAST 2003. EUROCAST 2003. Lecture Notes in Computer Science, vol 2809. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45210-2_38
Download citation
DOI: https://doi.org/10.1007/978-3-540-45210-2_38
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20221-9
Online ISBN: 978-3-540-45210-2
eBook Packages: Springer Book Archive