Abstract
In this paper we present P systems as a reliable computational modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the functioning of living cells. We will introduce two different strategies for the evolution of P systems, namely, Multi-compartmental Gillespie’s Algorithm based on the well known Gillespie’s Algorithm but running on more than one compartment; and Deterministic Waiting Times Algorithm, an exact deterministic method. In order to illustrate these two strategies we have modelled two biological systems: the EGFR Signalling Cascade and the Quorum Sensing System in the bacterium Vibrio Fischeri. Our simulations results show that for the former system a deterministic approach is valid whereas for the latter a stochastic approach like Multi-compartmental Gillespie’s Algorithm is necessary.
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References
Aho, A.V., Sethi, R., Ulmann, J.D.: Compilers: Principles, Techniques, and Tools. Addison-Wesley, Reading (1986)
Ardelean, I., Cavaliere, M.: Playing with a Probabilistic P Simulator: Mathematical and Biological Problems. In: Cavaliere, M., Martin-Vide, C., Păun, G. (eds.) Brainstorming Week on Membrane Computing, Tarragona, February 5-11 (2003); Tech. Rep. 26/03, Universitat Rovira i Virgili, Tarragona, Spain, pp. 37–45
Bernardini, F., Gheorghe, M., Muniyandi, R.C., Krasnogor, N., Pérez-Jiménez, M.J., Romero-Campero, F.J.: On P Systems as a Modelling Tool for Biological Systems. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 114–133. Springer, Heidelberg (2006)
Bernardini, F., Manca, V.: P Systems with Boundary Rules. In: [20], pp. 107–118 (2003)
Besozzi, D.: Computational and Modelling Power of P systems, Ph.D. Thesis, Università degli Studi di Milano, Milan, Italy (2004)
Bianco, L., Fontana, F., Franco, G., Manca, V.: P Systems for Biological Dynamics. In: Ciobanu, G., Păun, G., Pérez-Jiménez, M.J. (eds.) Applications of Membrane Computing, pp. 81–126. Springer, Heidelberg (2005)
Bianco, L., Fontana, F., Manca, V.: P Systems and the Modelling of Biochemical Oscillation. In: Pre-Proceedings of WMC6 - Vienna 2005, pp. 214–225 (2005)
Gibson, M.A., Bruck, J.: Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. Journal of Physical Chemistry 104(25), 1876–1889 (2000)
Gillespie, D.T.: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J. Comput. Physics 22, 403–434 (1976)
Gillespie, D.T.: Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Gillespie, D.T.: Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems. Journal of Chemical Physics 115(4), 1716–1733 (2001)
Gillespie, D.T.: Improved Leap-size Selection for Accelerated Stochastic Simulation. Journal of Chemical Physics 119(16), 8229–8234 (2003)
Karwowski, R., Prusinkiewicz, P.: Design and Implementation of the L+C Modelling Language. Electronics Notes in Theoretical Computer Science 82(2), 1–19 (2003)
Meng, T.C., Somani, S., Dhar, P.: Modelling and Simulation of Biological Systems with Stochasticity. In: Silico Biology, vol. 4, p. 0024 (2004)
Milner, R.: Communicating and Mobile System: The π-Calculus. Cambridge University Press, Cambridge (1999)
Moehren, G., et al.: Temperature Dependence of the Epidermal Growth Factor Receptor Signaling Network Can Be Accounted for by a Kinetic Model. Biochemistry 41, 306–320 (2002)
Păun, A., Păun, G.: The Power of Communication: P Systems with Symport/Antiport. New Generation Computing 20(3), 295–305 (2002)
Păun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)
Păun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002)
Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.): WMC 2002. LNCS, vol. 2597. Springer, Heidelberg (2003)
Philips, A., Cardelli., L.: A Correct Abstract Machine for the Stochastic Pi-calculus. Electronical Notes in Theoretical Computer Science (to appear, 2004)
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)
Schoeberl, B., et al.: Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors. Nature Biotech. 20, 370–375 (2002)
Stundzia, A.B., Lumsden, C.J.: Stochastic Simulation of Coupled Reaction-Diffusion Processes. Journal of Computational Physics 127, 196–207 (1996)
Nottingham Quorum Sensing Web Site, http://www.nottingham.ac.uk/quorum/
ISI Web Site (2003) html, http://esi-topics.com/erf/october
Scilab Web Pages: http://scilabsoft.inria.fr
The P Systems Web Page: http://psystems.disco.unimib.it
The Stochastic Pi-Machine: http://www.doc.ic.ac.uk/~anp/spim/
SciLab Web Site, http://scilabsoft.inria.fr/
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Pérez-Jiménez, M.J., Romero-Campero, F.J. (2006). P Systems, a New Computational Modelling Tool for Systems Biology. In: Priami, C., Plotkin, G. (eds) Transactions on Computational Systems Biology VI. Lecture Notes in Computer Science(), vol 4220. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880646_8
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DOI: https://doi.org/10.1007/11880646_8
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-45779-4
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