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Extended Simulation and Verification Platform for Kernel P Systems

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Membrane Computing (CMC 2014)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8961))

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Abstract

Kernel P systems integrate in a coherent and elegant manner many of the features of different P system variants, successfully used for modelling various applications. In this paper, we present our initial attempt to extend the software framework developed to support kernel P systems: a formal verification tool based on the NuSMV model checker and a large scale simulation environment based on FLAME. The use of these two tools for modelling and analysis of biological systems is illustrated with a synthetic biology example.

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References

  1. Bakir, M.E., Konur, S., Gheorghe, M., Niculescu, I., Ipate, F.: High performance simulations of kernel P systems. In: The 16th IEEE International Conference on High Performance Computing and Communications (2014)

    Google Scholar 

  2. Basu, S., Mehreja, R., Thiberge, S., Chen, M.T., Weiss, R.: Spatio-temporal control of gene expression with pulse-generating networks. PNAS 101(17), 6355–6360 (2004)

    Article  Google Scholar 

  3. Blakes, J., Twycross, J., Konur, S., Romero-Campero, F.J., Krasnogor, N., Gheorghe, M.: Infobiotics Workbench: A P systems based tool for systems and synthetic biology. In: [7], pp. 1–41. Springer (2014)

    Google Scholar 

  4. Cimatti, A., Clarke, E., Giunchiglia, E., Giunchiglia, F., Pistore, M., Roveri, M., Sebastiani, R., Tacchella, A.: NuSMV 2: An opensource tool for symbolic model checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, p. 359. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  5. Dragomir, C., Ipate, F., Konur, S., Lefticaru, R., Mierla, L.: Model checking kernel P systems. In: Alhazov, A., Cojocaru, S., Gheorghe, M., Rogozhin, Yu., Rozenberg, G., Salomaa, A. (eds.) CMC 2013. LNCS, vol. 8340, pp. 151–172. Springer, Heidelberg (2014)

    Chapter  Google Scholar 

  6. FLAME: Flexible large-scale agent modeling environment. http://www.flame.ac.uk/

  7. Frisco, P., Gheorghe, M., Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing in Systems and Synthetic Biology. Springer (2014)

    Google Scholar 

  8. Gheorghe, M., Ipate, F., Dragomir, C., Mierlă, L., Valencia-Cabrera, L., García-Quismondo, M., Pérez-Jiménez, M.J.: Kernel P systems - Version 1. 12th BWMC, pp. 97–124 (2013)

    Google Scholar 

  9. Gillespie, D.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics 22(4), 403–434 (1976)

    Article  MathSciNet  Google Scholar 

  10. Holzmann, G.J.: The model checker SPIN. IEEE Transactions on Software Engineering 23(5), 275–295 (1997)

    Article  MathSciNet  Google Scholar 

  11. Ipate, F., Bălănescu, T., Kefalas, P., Holcombe, M., Eleftherakis, G.: A new model of communicating stream X-machine systems. Romanian Journal of Information Science and Technology 6, 165–184 (2003)

    Google Scholar 

  12. Konur, S., Gheorghe, M., Dragomir, C., Ipate, F., Krasnogor, N.: Conventional verification for unconventional computing: a genetic XOR gate example. Fundamenta Informaticae (2014)

    Google Scholar 

  13. Konur, S., Gheorghe, M., Dragomir, C., Mierla, L., Ipate, F., Krasnogor, N.: Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems. ACS Synthetic Biology (2014)

    Google Scholar 

  14. KPWorkbench. http://kpworkbench.org

  15. Niculescu, I.M., Gheorghe, M., Ipate, F., Stefanescu., A.: From kernel P systems to X-machines and FLAME. Journal of Automata, Languages and Combinatorics (to appear, 2014)

    Google Scholar 

  16. Păun, Gh.: Computing with membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)

    Google Scholar 

  17. Păun, Gh., Rozenberg, G., Salomaa, A. (eds.): The Oxford Handbook of Membrane Computing. Oxford University Press (2010)

    Google Scholar 

  18. Romero-Campero, F.J., Twycross, J., Cao, H., Blakes, J., Krasnogor, N.: A multiscale modeling framework based on P systems. In: Corne, D.W., Frisco, P., Păun, Gh., Rozenberg, G., Salomaa, A. (eds.) WMC 2008. LNCS, vol. 5391, pp. 63–77. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  19. 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: The 16th IEEE International Conference on High Performance Computing and Communications (2014)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Sheffield, Regent Court, Portobello Street, Sheffield, S1 4DP, UK

    Mehmet E. Bakir & Savas Konur

  2. Department of Computer Science, University of Bucharest, Str. Academiei nr. 14, 010014, Bucharest, Romania

    Florentin Ipate & Laurentiu Mierla

  3. Department of Computer Science, University of Pitesti, Str. Targul din Vale, nr.1, 110040, Pitesti, Arges, Romania

    Ionut Niculescu

Authors
  1. Mehmet E. Bakir
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  2. Florentin Ipate
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  3. Savas Konur
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  4. Laurentiu Mierla
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  5. Ionut Niculescu
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Corresponding author

Correspondence to Savas Konur .

Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Sheffield, Sheffield, United Kingdom

    Marian Gheorghe

  2. Leiden Inst. Advanced Computer Science, Leiden University, Leiden, The Netherlands

    Grzegorz Rozenberg

  3. Turku Center for Computer Science, Turku, Finland

    Arto Salomaa

  4. Dept. Mathematics & Computer Science, Silesian University, Opava, Czech Republic

    Petr Sosík

  5. D.I.S.Co, University of Milan-Bicocca, Milan, Italy

    Claudio Zandron

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Bakir, M.E., Ipate, F., Konur, S., Mierla, L., Niculescu, I. (2014). Extended Simulation and Verification Platform for Kernel P Systems. In: Gheorghe, M., Rozenberg, G., Salomaa, A., Sosík, P., Zandron, C. (eds) Membrane Computing. CMC 2014. Lecture Notes in Computer Science(), vol 8961. Springer, Cham. https://doi.org/10.1007/978-3-319-14370-5_10

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  • DOI: https://doi.org/10.1007/978-3-319-14370-5_10

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-14369-9

  • Online ISBN: 978-3-319-14370-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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