Abstract
In this work we analyse and compare Hybrid Functional Petri Nets [10], an extension of Petri Nets [12] for biopathways simulation, and Metabolic P Systems [8,9]. An introduction to both of them is given, together with highlights about respective similarities and differences for biopathways modelling. The case study of glycolytic pathway with the lac operon gene regulatory mechanism was modeled by traditional Petri Nets in [6] and recently by Hybrid Functional Petri Nets in [10,4]. This model is here mapped into an MP system having the same dynamics.
.
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
Bianco, L., Fontana, F., Franco, G., Manca, V.: P Systems for Biological Dynamics. In: Ciobanu, G., et al. (eds.) Applications of Membrane Computing. Springer, Heidelberg (2006)
Bianco, L., Manca, V., Marchetti, L., Petterlini, M.: Psim: a Simulator for Biomolecular Dynamics Based on P Systems. In: IEEE Congress on Evolutionary Computation, September 25-28 (2007)
David, R., Alla, H.: On Hybrid Petri Nets. Discrete Event Dynamic Systems 11(1-2), 9–40 (2001)
Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.: Constructing Biological Pathway Models with Hybrid Functional Petri Nets. In Silico Biology 4, 23 (2004)
Fontana, F., Manca, V.: Discrete Solution of Differential Equations by Metabolic P Systems. Theoretical Computer Science 372, 165–182 (2007)
Hofestädt, R.: A Petri Net Application of Metabolic Processes. Journal of System Analysis, Modeling and Simulation 16, 113–122 (1994)
Manca, V.: Discrete Simulations of Biochemical Dynamics. In: Garzon, M., Yan, H. (eds.) Preliminary Proceedings of the 13th International Meeting on DNA Computing, Memphis, TN, June 4-8, University of Memphis (2007)
Manca, V.: The Metabolic Algorithm for P Systems: Principles and Applications. TCS 404(1-2), 142–155 (2008)
Manca, V., Bianco, L.: Biological Networks in Metabolic P Systems. BioSystems 91(3), 489–498 (2008)
Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.: Biopathways Representation and Simulation on Hybrid Functional Petri Net. In Silico Biology 3, 32 (2003)
Păun, G.: Membrane Computing. An Introduction. Springer, Berlin (2002)
Reisig, W.: Petri Nets: An Introduction. EATCS, Monographs on Theoretical Computer Science (1985)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Tokyo
About this paper
Cite this paper
Castellini, A., Franco, G., Manca, V. (2009). Toward a Representation of Hybrid Functional Petri Nets by MP Systems. In: Suzuki, Y., Hagiya, M., Umeo, H., Adamatzky, A. (eds) Natural Computing. Proceedings in Information and Communications Technology, vol 1. Springer, Tokyo. https://doi.org/10.1007/978-4-431-88981-6_3
Download citation
DOI: https://doi.org/10.1007/978-4-431-88981-6_3
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-88980-9
Online ISBN: 978-4-431-88981-6
eBook Packages: Computer ScienceComputer Science (R0)