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

  • David Gilbert
  • Monika Heiner
  • Fei Liu
  • Nigel Saunders
Part of the Lecture Notes in Computer Science book series (LNCS, 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.

Keywords

Coloured Petri nets qualitative stochastic continuous hybrid Petri nets spatial modelling biomolecular networks Systems Biology BioModel Engineering 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • David Gilbert
    • 1
  • Monika Heiner
    • 2
  • Fei Liu
    • 3
  • Nigel Saunders
    • 1
  1. 1.School of Information Systems, Computing and MathematicsBrunel UniversityUxbridgeUK
  2. 2.Computer Science InstituteBrandenburg University of TechnologyCottbusGermany
  3. 3.Harbin Institute of TechnologyHarbinChina

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