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Conventional Verification for Unconventional Computing : a Genetic XOR Gate Example

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Języki publikacji
EN
Abstrakty
EN
As unconventional computation matures and non-standard programming frameworks are demonstrated, the need for formal verification will become more prevalent. This is so because “programming” in unconventional substrates is difficult. In this paper we show how conventional verification tools can be used to verify unconventional programs implementing a logical XOR gate.
Wydawca
Rocznik
Strony
97--110
Opis fizyczny
Bibliogr. 32 poz., rys., tab., wykr.
Twórcy
autor
  • Department of Computer Science, University of Sheffield, Sheffield, UK
autor
  • Department of Computer Science, University of Sheffield, Sheffield, UK
autor
  • Department of Computer Science, University of Sheffield, Sheffield, UK
autor
  • Department of Computer Science, University of Bucharest, Bucharest, Romania
autor
  • School of Computing Science, Newcastle University, Newcastle, UK
Bibliografia
  • [1] Baier, C., Haverkort, B., Hermanns, H., Katoen, J.: Model Checking Algorithms for Continuous-time Markov Chains, IEEE Transactions on Software Engineering, 29(6), 2003, 524–541.
  • [2] Bakir, M. E., Ipate, F., Konur, S., Mierlä, L., Niculescu, I.: Extended Simulation and Verification Platform for Kernel P Systems, 15th International Conference on Membrane Computing, 2014.
  • [3] Bakir, M. E., Konur, S., Gheorghe, M., Niculescu, I., Ipate, F.: High Performance Simulations of Kernel P Systems, The 16th IEEE International Conference on High Performance Computing and Communications, 2014.
  • [4] Beal, J., Phillips, A., Densmore, D., Cai, Y.: High-Level Programming Languages for Biomolecular Systems, in: Design and Analysis of Biomolecular Circuits, Springer New York, 2011, 225–252.
  • [5] Bernardini, F., Gheorghe, M., Romero-Campero, F., Walkinshaw, N.: A Hybrid Approach to Modelling Biological Systems, Proc. 8th Workshop on Membrane Computing, 4860, Springer, 2007.
  • [6] 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: [11], Springer, 2014, 1–41.
  • [7] Blakes, J., Twycross, J., Romero-Campero, F. J., Krasnogor, N.: The Infobiotics Workbench: An Integrated In Silico Modelling Platform for Systems and Synthetic Biology, Bioinformatics, 27(123), 2011, 3323 – 3324.
  • [8] Chaplin, J. C., Russell, N. A., Krasnogor, N.: Implementing Conventional Logic Unconventionally: Photochromic Molecular Populations as Registers and Logic Gates, Biosystems, 109(1), 2012, 35 – 51.
  • [9] Donaldson, R., Gilbert, D.: A Monte Carlo Model Checker for Probabilistic LTL with Numerical Constraints, Technical report, Bioinformatics Research Centre, University of Glasgow, Glasgow, 2008.
  • [10] Dragomir, C., Ipate, F., Konur, S., Lefticaru, R., Mierlă, L.: Model Checking Kernel P Systems, 14th International Conference on Membrane Computing, 8340, Springer, 2013.
  • [11] Frisco, P., Gheorghe, M., Pérez-Jiménez, M. J., Eds.: Applications of Membrane Computing in Systems and Synthetic Biology, Springer, 2014.
  • [12] 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, 2013, 97–124.
  • [13] Gheorghe, M., Ipate, F., Lefticaru, R., Pérez-Jiménez, M. J., Ţurcanu, A., Valencia-Cabrera, L., Garcıa-Quismondo, M., Mierlă, L.: 2-Col Problem Modelling Using Simple Kernel P Systems, International Journal of Computer Mathematics, 90(4), 2012, 816–830.
  • [14] Gillespie, D.: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions, Journal of Computational Physics, 22(4), 1976, 403–434.
  • [15] Hansson, H., Jonsson, B.: A Logic for Reasoning about Time and Reliability, Formal Aspects of Computing, 6, 1994, 102–111.
  • [16] Hinton, A., Kwiatkowska, M., Norman, G., Parker, D.: PRISM: A Tool for Automatic Verification of Probabilistic Systems, in: Proc. TACAS, vol. 3920 of LNCS, Springer, 2006, 441–444.
  • [17] Holzmann, G. J.: The Model Checker SPIN, IEEE Transactions on Software Engineering, 23(5), 1997, 275–295.
  • [18] 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, To Appear.
  • [19] Pasparakis, G., Vamvakaki, M., Krasnogor, N., Alexander, C.: Diol-boronic Acid Complexes Integrated by Responsive Polymers - A Route to Chemical Sensing and Logic Operations, Soft Matter, 4(20), 2009, 3839 – 3841.
  • [20] Păun, G.: Computing with Membranes, Journal of Computer and System Sciences, 61(1), 2000, 108–143.
  • [21] Păun, G., Rozenberg, G., Salomaa, A., Eds.: The Oxford Handbook of Membrane Computing, Oxford University Press, 2009.
  • [22] 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), 2011, 207–211.
  • [23] Romero-Campero, F. J., Gheorghe, M., Ciobanu, G., Auld, J. M., Pérez-Jiménez, M. J.: Cellular Modelling Using P Systems and Process Algebra, Progress in Natural Science, 17, 2007, 375–383.
  • [24] Romero-Campero, F. J., Twycross, J., Camara, M., Bennett, M., Gheorghe, M., Krasnogor, N.: Modular Assembly of Cell Systems Biology Models using P Systems, International Journal of Foundations of Computer Science, 20(3), 2009, 427–442.
  • [25] Romero-Campero, F. J., Twycross, J., Cao, H., Blakes, J., Krasnogor, N.: A Multiscale Modeling Framework Based on P Systems, in: Membrane Computing, vol. 5391 of LNCS, Springer, 2009, 63–77.
  • [26] Rozenberg, G., Bäck, T., Kok, J. N., Eds.: Handbook of Natural Computing, Springer, 2012.
  • [27] 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, The 16th IEEE International Conference on High Performance Computing and Communications, 2014.
  • [28] Smaldon, J., Romero-Campero, F. J., Fernandez Trillo, F., Gheorghe, M., Alexander, C., Krasnogor, N.: A Computational Study of Liposome Logic: Towards Cellular Computing from the Bottom Up, Systems and Synthetic Biology, 4(3), 2010, 157 – 179.
  • [29] Tamsir, A., Tabor, J. J., Voigt, C. A.: Robust Multicellular Computing Using Genetically Encoded NOR Gates and Chemical ’Wires’, Nature, 469(7329), 2011, 212–215.
  • [30] Terrazas, G., Lui, L. T., Krasnogor, N.: Spatial Computation and Algorithmic Information Content in Non-DNA based Molecular Self-assembly, 6th International Workshop on Spatial Computing, 2013.
  • [31] Xor gate, url: http://staffwww.dcs.shef.ac.uk/people/s.konur/models/xor.
  • [32] Younes, H. L. S., Simmons, R. G.: Probabilistic Verification of Discrete Event Systems Using Acceptance Sampling, in: Computer Aided Verification, vol. 2404 of Lecture Notes in Computer Science, Springer Berlin Heidelberg, 2002, 223–235.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-0e67da55-83a3-4d85-a781-4abd0029b6c1
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