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Constructing and visualizing chemical reaction networks from pi-calculus models

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Formal Aspects of Computing

Abstract

The π-calculus, in particular its stochastic version the stochastic π-calculus, is a common modeling formalism to concisely describe the chemical reactions occurring in biochemical systems. However, it remains largely unexplored how to transform a biochemical model expressed in the stochastic π-calculus back into a set of meaningful reactions. To this end, we present a two step approach of first translating model states to reaction sets and then visualizing sequences of reaction sets, which are obtained from state trajectories, in terms of reaction networks. Our translation from model states to reaction sets is formally defined and shown to be correct, in the sense that it reflects the states and transitions as they are derived from the continuous time Markov chain-semantics of the stochastic π-calculus. Our visualization concept combines high level measures of network complexity with interactive, table-based network visualizations. It directly reflects the structures introduced in the first step and allows modelers to explore the resulting simulation traces by providing both: an overview of a network’s evolution and a detail inspection on demand.

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Authors and Affiliations

  1. Lifl (CNRS UMR8022), University of Lille 1, Lille, France

    Mathias John

  2. Graz University of Technology, Graz, Austria

    Hans-Jörg Schulz

  3. Institute for Computer Science, University of Rostock, Rostock, Germany

    Heidrun Schumann & Adelinde M. Uhrmacher

  4. Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Potsdam, Germany

    Andrea Unger

Authors
  1. Mathias John
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  2. Hans-Jörg Schulz
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  3. Heidrun Schumann
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  4. Adelinde M. Uhrmacher
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  5. Andrea Unger
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Correspondence to Mathias John.

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Jim Woodcock

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John, M., Schulz, HJ., Schumann, H. et al. Constructing and visualizing chemical reaction networks from pi-calculus models. Form Asp Comp 25, 723–742 (2013). https://doi.org/10.1007/s00165-011-0209-0

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  • DOI: https://doi.org/10.1007/s00165-011-0209-0

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