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Modelling and Analysis of E. coli Respiratory Chain

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Applications of Membrane Computing in Systems and Synthetic Biology

Part of the book series: Emergence, Complexity and Computation ((ECC,volume 7))

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Abstract

In this chapter we present some results obtained in the study of the bacterium E. coli related to its behavior at different level of oxygen in the environment. The biological model is expressed in terms of different molecules and their reactions. First, an agent-based model of E. coli is implemented in the FLAME framework for multi-agents and some simulation results are given. Each agent is represented by an X-machine and the model corresponds to communicating X-machines. Then this model is transformed into a kernel P system. This kernel P system is implemented in the Rodin platform and in Spin and some properties are verified using the associated model checkers. Formulated using the LTL formalism, the verified properties refer to the variation of the number of different molecules as a result of the occurring reactions. Our main contribution is a simplified model of E. coli that preserves the main properties of the initial model, and can be formally verified using a model checker.

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References

  1. FLAME web site. http://flame.ac.uk

  2. MuVeT web site. http://muvet.ifsoft.ro/e-coli.html

  3. ProB web site. http://www.stups.uni-duesseldorf.de/ProB

  4. Spin web site. http://spinroot.com

  5. SUMO project. http://sysmo-sumo.mpi-magdeburg.mpg.de/trac/wiki/public

  6. J.-R. Abrial, Modeling in Event-B. System and software engineering. (Cambridge University Press, New York, 2010)

    Google Scholar 

  7. J.-R. Abrial, S. Hallerstede, Refinement, decomposition, and instantiation of discrete models: Application to Event-B. Fundam. Informaticae 77, 1–28 (2007)

    MATH  MathSciNet  Google Scholar 

  8. O. Andrei, M. Calder, Trend-based analysis of a population model of the AKAP scaffold protein. Trans. Comput. Syst. Biol. 7625, 1–25 (2012)

    Article  Google Scholar 

  9. O. Andrei, G. Ciobanu, D. Lucanu, A rewriting logic framework for operational semantics of membrane systems. Theor. Comput. Sci. 373(3), 163–181 (2007)

    Article  MATH  MathSciNet  Google Scholar 

  10. D. Benque, S. Bourton, C. Cockerton, B. Cook, J. Fisher, S. Ishtiaq, N. Piterman, A. Taylor, M. Vardi,in Proceedings of CAV’12, BMA: visual tool for modeling and analyzing biological networks. vol. 7358 of LNCS (Springer, 2012), pp. 686–692

    Google Scholar 

  11. F. Bernardini, M. Gheorghe, F.J. Romero-Campero, N. Walkinshaw, in WMC 2007, A hybrid approach to modeling biological systems, vol. 4860 of LNCS (Springer, 2007), pp. 138–159

    Google Scholar 

  12. J. Blakes, J. Twycross, F.J. Romero-Campero, N. Krasnogor, The Infobiotics workbench: an integrated in silico modelling platform for systems and synthetic biology. Bioinformatics 27(23), 3323–3324 (2011)

    Article  Google Scholar 

  13. G. Ciobanu, M.J. Pérez-Jiménez, G. Păun, (eds.), Applications of Membrane Computing. Natural Computing Series (Springer, Heidelberg, 2006)

    Google Scholar 

  14. E. Csuhaj-Varjú, M. Gheorghe, M. Stannett, in Proceedings of UCNC’12. P systems controlled by general topologies, vol. 7445 of LNCS (Springer, 2012), pp. 70–81

    Google Scholar 

  15. D. Díaz-Pernil, C. Graciani, M. Gutierrez-Naranjo, I. Pérez-Hurtado, M. Pérez-Jiménez. Software for P systems, in The Oxford Handbook of Membrane Computing, ed. by Gh. Păun, G. Rozenberg, A. Salomaa (Oxford University Press, Oxford, 2010), pp. 118–143

    Google Scholar 

  16. D. Díaz-Pernil, I. Pérez-Hurtado, M. Pérez-Jiménez, A. Riscos-Núñez, in Proceedings of WMC’08. A P-Lingua programming environment for membrane computing, vol. 5391 of LNCS (Springer, Heidelberg, 2008), pp. 187–203

    Google Scholar 

  17. S. Eilenberg, Automata, Languages and Machines (Academic Press, New York, 1994)

    Google Scholar 

  18. M. Gheorghe, F. Ipate, C. Dragomir. A kernel P system, in Proceedings of BWMC10. Fénix Editora, Seville, 2012, pp. 153–170

    Google Scholar 

  19. M. Gheorghe, F. Ipate, R. Lefticaru, C. Dragomir, in Proceedings of CMC’10, An integrated approach to P systems formal verification, (ProBusiness Verlag, Heidelberg, 2010), pp. 225–238

    Google Scholar 

  20. M. Gheorghe, F. Ipate, R. Lefticaru, M.J. Pérez-Jiménez, A. Turcanu, L. Mierla, L. Valencia Cabrera, F.M. Garcia-Quismondo, 3-Col problem modelling using simple kernel P systems. Int. J. Comput. Math. 90(4), 816–830 (2013)

    Article  MATH  MathSciNet  Google Scholar 

  21. A. Hinton, M. Z. Kwiatkowska, G. Norman, D. Parker, in Proceedings of TACAS’06. PRISM: a tool for automatic verification of probabilistic systems, vol. 3920 of LNCS (Springer, Heidelberg, 2006), pp. 441–444

    Google Scholar 

  22. M. Holcombe, X-machines as a basis for dynamic system specification. Softw. Eng. J. 3(2), 69–76 (1988)

    Article  Google Scholar 

  23. M. Holcombe et al., Modelling complex biological systems using an agent-based approach. Integr. Biol. 4, 53–64 (2012)

    Article  Google Scholar 

  24. G. Holzmann, The model checker SPIN. IEEE Trans. Softw. Eng. 5(23), 279–295 (1997)

    Article  Google Scholar 

  25. F. Ipate, T. Balanescu, P. Kefalas, M. Holcombe, G. Eleftherakis, A new model of communicating stream X-machine systems. Rom. J. Inf. Sci. Technol. 6(1–2), 165–184 (2003)

    Google Scholar 

  26. F. Ipate, R. Lefticaru, L. Mierla, L. Valencia Cabrera, H. Han, G. Zhang, C. Dragomir, M. J. Pérez-Jiménez, M. Gheorghe, in Proceedings of BIC-TA’13. Kernel P systems: applications and implementations, vol. 202 of Advances in Intelligent Systems and Computing (Springer, 2013), pp. 1081–1089

    Google Scholar 

  27. F. Ipate, R. Lefticaru, C. Tudose, Formal verification of P systems using SPIN. Int. J. Found Comput. Sci. 22(1), 133–142 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  28. F. Ipate, A. Turcanu, in Proceedings of BWMC9. Modelling, verification and testing of P systems using Rodin and ProB, (Fénix Editora, Seville, 2011), pp. 209–220

    Google Scholar 

  29. M. Kwiatkowska, G. Norman, D. Parker. Symbolic Systems Biology, chapter Probabilistic Model Checking for Systems Biology. (Jones and Bartlett, 2010), pp. 31–59

    Google Scholar 

  30. M. Leuschel, M. Butler, ProB: an automated analysis toolset for the B method. Int. J. Softw.Tools for Technol. Transf. 10(2), 185–203 (2008)

    Article  Google Scholar 

  31. A. Obtulowicz, G. Paun, (In search of) Probabilistic P systems. Biosystems 70(2), 107–121 (2003)

    Article  Google Scholar 

  32. I. Pérez-Hurtado, L. V. Cabrera, M. J. Pérez-Jiménez, M. A. Colomer, in Proceedings of BIC-TA’10. MeCoSim: a general purpose software tool for simulating biological phenomena by means of P systems, (IEEE Xplore, 2010), pp. 637–643

    Google Scholar 

  33. G. Păun, Computing with membranes. J. Comput. Sys. Sci. 61(1), 108–143 (2000)

    Article  MATH  MathSciNet  Google Scholar 

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

    Google Scholar 

  35. P. Richmond, D. Walker, S. Coakley, D. Romano, High performance cellular level agent-based simulation with FLAME for the GPU. Briefings in Bioinf. 11(3), 334–347 (2010)

    Article  Google Scholar 

  36. A. Turcanu, F. Ipate, in Proceedings of CMC’11. Modelling, testing and verification of P systems with active membranes using Rodin and ProB, (Paris-Est University Press, Paris, 2011), pp. 459–468

    Google Scholar 

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Acknowledgments

This work was partially supported by the Romanian National Authority for Scientific Research, CNCS-UEFISCDI, via MuVeT project [2], code PN-II-ID-PCE-2011-3-0688

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Authors and Affiliations

  1. Department of Computer Science, University of Piteşti, Piteşti, Romania

    Adrian Ţurcanu, Laurenţiu Mierlă, Florentin Ipate & Alin Stefanescu

  2. Department of Computer Science, University of Bucharest, Bucharest, Romania

    Florentin Ipate

  3. Department of Computer Science, University of Sheffield, Sheffield, UK

    Hao Bai, Mike Holcombe & Simon Coakley

Authors
  1. Adrian Ţurcanu
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  2. Laurenţiu Mierlă
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  3. Florentin Ipate
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  4. Alin Stefanescu
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  5. Hao Bai
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  6. Mike Holcombe
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  7. Simon Coakley
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Correspondence to Adrian Ţurcanu .

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Editors and Affiliations

  1. The School of Mathematical and Computer Sciences, Heriot-Watt University, Eindhoven, United Kingdom

    Pierluigi Frisco

  2. The Department of Computer Science, University of Sheffield, Sheffield, United Kingdom

    Marian Gheorghe

  3. Department of Computer Science and Artificial Intelligence, University of Sevilla, Sevilla, Spain

    Mario J. Pérez-Jiménez

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Ţurcanu, A. et al. (2014). Modelling and Analysis of E. coli Respiratory Chain. In: Frisco, P., Gheorghe, M., Pérez-Jiménez, M. (eds) Applications of Membrane Computing in Systems and Synthetic Biology. Emergence, Complexity and Computation, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-03191-0_8

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  • DOI: https://doi.org/10.1007/978-3-319-03191-0_8

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-319-03191-0

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