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2017 | OriginalPaper | Buchkapitel

25. Kernel P Systems and Stochastic P Systems for Modelling and Formal Verification of Genetic Logic Gates

verfasst von : Marian Gheorghe, Savas Konur, Florentin Ipate

Erschienen in: Advances in Unconventional Computing

Verlag: Springer International Publishing

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Abstract

P systems are the computational models of membrane computing, a computing paradigm within natural computing area inspired by the structure and behaviour of the living cell. In this chapter, we discuss two variants of this model, a non-deterministic case, called kernel P (kP) systems, and a stochastic one, called stochastic P (sP) systems. For both we present specification languages and associated tools, including simulation and verification components. The expressivity and analysis power of these natural computing models will be used to illustrate the behaviour of two genetic logic gates.

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Vorheriges Kapitel Computational Properties of Cell Regulatory Pathways Through Petri Nets
Nächstes Kapitel On Improving the Expressive Power of Chemical Computation
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Literatur
1.
Bakir, M.E., Ipate, F., Konur, S., Mierlă, L., Niculescu, I.: Extended simulation and verification platform for kernel P systems. In: 15th International Conference on Membrane Computing. LNCS, vol. 8961, pp. 158–168. Springer, Heidelberg (2014)
2.
Bakir, M.E., Konur, S., Gheorghe, M., Niculescu, I., Ipate, F.: High performance simulations of kernel P systems. In: Proceedings of the 2014 IEEE 16th International Conference on High Performance Computing and Communication. HPCC ’14, pp. 409–412. France, Paris (2014)
3.
Beal, J., Lu, T., Weiss, R.: Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS One 6(8), e22490 (2011) CrossRef
4.
Beal, J., Phillips, A., Densmore, D., Cai, Y.: High-level programming languages for biomolecular systems. Design and Analysis of Biomolecular Circuits, pp. 225–252. Springer, New York (2011) CrossRef
5.
Bilitchenko, L., Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J.C., Densmore, D.: Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 6(4), e18882 (2011) CrossRef
6.
Blakes, J., Twycross, J., Konur, S., Romero-Campero, F., Krasnogor, N., Gheorghe, M.: Infobiotics workbench: a P systems based tool for systems and synthetic biology. In: Applications of Membrane Computing in Systems and Synthetic Biology. Emergence, Complexity and Computation, vol. 7, pp. 1–41. Springer, Heidelberg (2014)
7.
Cimatti, A., Clarke, E., Giunchiglia, E., Giunchiglia, F., Pistore, M., Roveri, M., Sebastiani, R., Tacchella, A.: NuSMV version 2: an open source tool for symbolic model checking. In: Proceedings of the International Conference on Computer-Aided Verification (CAV 2002). LNCS, vol. 2404, pp. 359–364. Springer, Denmark (2002)
8.
Ciobanu, G., Păun, Gh, Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing. Springer, Heidelberg (2006)
9.
Díaz-Pernil, D., Gutiérrez-Naranjo, M.A., Pérez-Jiménez, M.J.: A uniform family of tissue P systems with cell division solving 3-COL in a linear time. Theor. Comput. Sci. 404, 76–87 (2008) MathSciNetCrossRefMATH
10.
11.
Dragomir, C., Ipate, F., Konur, S., Lefticaru, R., Mierlă, L.: Model checking kernel P systems. In: 14th International Conference on Membrane Computing. LNCS, vol. 8340, pp. 151–172. Springer, Heidelberg (2013)
12.
Frisco, P., Gheorghe, M., Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing in Systems and Synthetic Biology. Springer, Heidelberg (2014)
13.
Gheorghe, M., Ipate, F., Dragomir, C.: Kernel P systems. In: 10th Brainstorming Week on Membrane Computing, pp. 153–170. Fénix Editora, Brazil (2012)
14.
Gheorghe, M., Ipate, F., Dragomir, C., Mierlă, L., Valencia-Cabrera, L., García-Quismondo, M., Pérez-Jiménez, M.J.: Kernel P systems - version 1. In: 11th Brainstorming Week on Membrane Computing, pp. 97–124. Fénix Editora, Brazil (2013)
15.
Gheorghe, M., Ipate, F., Lefticaru, R., Pérez-Jiménez, M.J., Ţurcanu, A., Valencia-Cabrera, L., García-Quismondo, M., Mierlă, L.: 3-Col problem modelling using simple kernel P systems. Int. J. Comput. Math. 90(4), 816–830 (2012) MathSciNetCrossRefMATH
16.
Gheorghe, M., Păun, G., Pérez-Jiménez, M.J., Rozenberg, G.: Research frontiers of membrane computing: open problems and research topics. Int. J. Found. Comput. Sci. 24, 547–624 (2013) MathSciNetCrossRefMATH
17.
Gillespie, D.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22(4), 403–434 (1976) MathSciNetCrossRef
18.
Gimel’farb, G.L., Nicolescu, R., Ragavan, S.: P system implementation of dynamic programming stereo. J. Math. Imaging Vis. 47(1–2), 13–26 (2013) CrossRefMATH
19.
Hinton, A., Kwiatkowska, M., Norman, G., Parker, D.: PRISM: a tool for automatic verification of probabilistic systems. Proceedings of the TACAS. LNCS, vol. 3920, pp. 441–444. Springer, Heidelberg (2006)
20.
Konur, S., Gheorghe, M.: Property-driven methodology for formal analysis of synthetic biology systems. IEEE/ACM Trans. Comput. Biol. Bioinform. 12(2), 360–371 (2015) CrossRef
21.
Konur, S., Gheorghe, M., Dragomir, C., Ipate, F., Krasnogor, N.: Conventional verification for unconventional computing: a genetic XOR gate example. Fundamenta Informaticae 134(1–2), 97–110 (2014) MathSciNetMATH
22.
Konur, S., Gheorghe, M., Dragomir, C., Mierlă, L., Ipate, F., Krasnogor, N.: Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems. ACS Synth. Biol. 4(1), 83–92 (2015) CrossRef
23.
Konur, S., Ladroue, C., Fellermann, H., Sanassy, D., Mierla, L., Ipate, F., Kalvala, S., Gheorghe, M., Krasnogor, N.: Modeling and analysis of genetic boolean gates using Infobiotics Workbench. In: Verification of Engineered Molecular Devices and Programs, pp. 26–37. Vienna, Austria (2014)
24.
25.
26.
27.
28.
Păun, G., Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing. Oxford University Press, Oxford (2010)
29.
Pedersen, M., Phillips, A.: Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 6(Suppl 4), S437–S450 (2009)
30.
Regot, S., Macia, J., Conde, N., Furukawa, K., Kjellen, J., Peeters, T., Hohmann, S., de Nadal, E., Posas, F., Sole, R.: Distributed biological computation with multicellular engineered networks. Nature 469(7329), 207–211 (2011) CrossRef
31.
Romero-Campero, F., Twycross, J., Càmara, M., Bennett, M., Gheorghe, M., Krasnogor, N.: Modular assembly of cell systems biology models using P systems. Int. J. Found. Comput. Sci. 20(3), 427–442 (2009) MathSciNetCrossRefMATH
32.
Rozenberg, G., Bäck, T., Kok, J.N. (eds.): Handbook of Natural Computing. Springer, Heidelberg (2012)
33.
Sanassy, D., Fellermann, H., Krasnogor, N., Konur, S., Mierlă, L., Gheorghe, M., Ladroue, C., Kalvala, S.: Modelling and stochastic simulation of synthetic biological boolean gates. In: Proceedings of the 2014 IEEE 16th International Conference on High Performance Computing and Communication. HPCC ’14, pp. 404–408. France, Paris (2014)
34.
Tamsir, A., Tabor, J.J., Voigt, C.A.: Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469(7329), 212–215 (2011) CrossRef
Metadaten
Titel
Kernel P Systems and Stochastic P Systems for Modelling and Formal Verification of Genetic Logic Gates
verfasst von
Marian Gheorghe
Savas Konur
Florentin Ipate
Copyright-Jahr
2017
Buch
Advances in Unconventional Computing

Print ISBN: 978-3-319-33923-8

Electronic ISBN: 978-3-319-33924-5

Copyright-Jahr: 2017

DOI
https://doi.org/10.1007/978-3-319-33924-5_25