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Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology

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Book cover Application and Theory of Petri Nets and Concurrency (PETRI NETS 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7927))

Abstract

In this paper we introduce a technique to encode spatial attributes of dynamic systems using coloured Petri nets and show how it can be applied to biological systems within the spirit of BioModel Engineering. Our approach can be equally applied to qualitative, stochastic, continuous or hybrid models of the same physical system, and can be used as the basis for multiscale modelling. We illustrate our approach with two case studies, one from the continuous and one from the stochastic paradigm. In this paper we only discuss the case of finite colours, and by unfolding our method can take advantage of all the analytical machinery and simulation techniques that have been developed for the uncoloured family of Petri net classes.

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Author information

Authors and Affiliations

  1. School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, Middlesex, UB8 3PH, UK

    David Gilbert & Nigel Saunders

  2. Computer Science Institute, Brandenburg University of Technology, Postbox 10 13 44, 03013, Cottbus, Germany

    Monika Heiner

  3. Harbin Institute of Technology, West Dazhi Street 92, 150001, Harbin, China

    Fei Liu

Authors
  1. David Gilbert
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  2. Monika Heiner
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  3. Fei Liu
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  4. Nigel Saunders
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Editor information

Editors and Affiliations

  1. Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, María de Luna, 1, 50018, Zaragoza, Spain

    José-Manuel Colom

  2. Fernuniversität Hagen, IZ, Universitätsstraße 1, 58097, Hagen, Germany

    Jörg Desel

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Gilbert, D., Heiner, M., Liu, F., Saunders, N. (2013). Colouring Space - A Coloured Framework for Spatial Modelling in Systems Biology. In: Colom, JM., Desel, J. (eds) Application and Theory of Petri Nets and Concurrency. PETRI NETS 2013. Lecture Notes in Computer Science, vol 7927. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38697-8_13

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  • DOI: https://doi.org/10.1007/978-3-642-38697-8_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38696-1

  • Online ISBN: 978-3-642-38697-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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