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An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation

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Advances in Unconventional Computing

Part of the book series: Emergence, Complexity and Computation ((ECC,volume 23))

Abstract

Recent advances Synthetic Biology are ushering a new practical computational substrate based on programmable information processing via biological cells. Due to the difficulties in orchestrating complex programmes using myriads of relatively simple, limited and highly stochastic processors such as living cells, robust computational technology to specify, simulate, analyse and compile cellular programs are in demand. We provide the Infobiotics Workbench (Ibw) tool, a software platform developed to model and analyse stochastic compartmentalized systems, which permits using various computational techniques, such as modelling, simulation, verification and biocompilation. We report here the details of our work for modelling, simulation and, for the first time, biocompilation, while verification is reported elsewhere in this book. We consider some basic genetic logic gates to illustrate the main features of the Ibw platform. Our results show that membrane computing provides a suitable formalism for building synthetic biology models. The software platform we developed permits analysing biological systems through the computational methods integrated into the workbench, providing significant advantages in terms of time, and enhanced understanding of biological functionality.

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Acknowledgments

SKo and MG acknowledge the EPSRC (EP/I031812/1) support. CL and SKa are supported by EPSRC (EP/I03157X/1). HF, DS and NK’s work is supported by EPSRC (EP/I031642/1, EP/I031642/2, EP/J004111/1, EP/J004111/2, EP/L001489/1 and EP/L001489/2).

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Authors and Affiliations

  1. School of Electrical Engineering and Computer Science, University of Bradford, Richmond Road, Bradford, BD7 1DP, UK

    Savas Konur & Marian Gheorghe

  2. Faculty of Mathematics and Computer Science, University of Bucharest, Str. Academiei Nr.14, Sector 1, C.P., 010014, Bucharest, Romania

    Larentiu Marian Mierla

  3. Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK

    Christophe Ladroue & Sara Kalvala

  4. School of Computing Science, Newcastle University, Claremont Tower, Newcastle-upon-Tyne, NE1 7RU, UK

    Harold Fellermann, Daven Sanassy & Natalio Krasnogor

Authors
  1. Savas Konur
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  2. Harold Fellermann
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  3. Larentiu Marian Mierla
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  4. Daven Sanassy
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  5. Christophe Ladroue
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  6. Sara Kalvala
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  7. Marian Gheorghe
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  8. Natalio Krasnogor
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Corresponding author

Correspondence to Natalio Krasnogor .

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  1. Unconventional ComputingCentre, University of the Westof England Unconventional ComputingCentre, Bristol, United Kingdom

    Andrew Adamatzky

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Konur, S. et al. (2017). An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation. In: Adamatzky, A. (eds) Advances in Unconventional Computing. Emergence, Complexity and Computation, vol 23. Springer, Cham. https://doi.org/10.1007/978-3-319-33921-4_25

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  • DOI: https://doi.org/10.1007/978-3-319-33921-4_25

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