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Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology

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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))

Abstract

This chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework. The Workbench incorporates three important features, simulation, model checking and optimisation. Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and synthetic biology research.

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Notes

  1. 1.

    http://www.infobiotics.org

  2. 2.

    The \(\mathbf{P}_{\sim r}\) operator is the probabilistic counter-part of path-quantifiers \(\forall \) and \(\exists \) of CTL.

  3. 3.

    At the moment, the NLQ tool is not integrated into the Infobiotics Workbench. But, the properties it generates can be directly used in IBW’s model checking component.

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Acknowledgments

JB, JT, SK, NK and MG acknowledge the support provided for synthetic biology research by EPSRC ROADBLOCK project (EP/I031642/1 & EP/I031812/1), EPSRC AUDACIOUS project (EP/J004111/1) and FP7 STREP CADMAD project. JR-C acknowledges support from Cellular Computing Applications into Systems and Synthetic Biology, TIN2009-13192, and Computational Modelling and Simulation in Systems Biology, P08-TIC-04200. MG was also partially supported by the MuVet project, (CNCS–UEFISCDI), grant number PN-II-ID-PCE-2011-3-0688. Some parts of this paper are based on the first author’s Ph.D. thesis [13].

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Authors and Affiliations

  1. ICOS Research Group, School of Computer Science, University of Nottingham, Nottingham, UK

    Jonathan Blakes, Jamie Twycross & Natalio Krasnogor

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

    Savas Konur & Marian Gheorghe

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

    Francisco Jose Romero-Campero

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  1. Jonathan Blakes
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  2. Jamie Twycross
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  3. Savas Konur
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  4. Francisco Jose Romero-Campero
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  5. Natalio Krasnogor
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  6. Marian Gheorghe
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Correspondence to Jonathan Blakes .

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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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Blakes, J., Twycross, J., Konur, S., Romero-Campero, F.J., Krasnogor, N., Gheorghe, M. (2014). Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology. 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_1

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  • DOI: https://doi.org/10.1007/978-3-319-03191-0_1

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