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Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy

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Modeling Biomolecular Site Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1945))

Abstract

This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.

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Acknowledgements

We thank Guy Melançon and Olivier Namet for their work in the initial Porgy project (2009–2012); their ideas and enthusiasm were invaluable during the early stages of development of this tool. We also thank Jason Vallet for implementing several features of Porgy and writing the documentation.

Author information

Authors and Affiliations

  1. School of Computing Science, University of Glasgow, Glasgow, UK

    Oana Andrei

  2. Department of Informatics, King’s College London, London, UK

    Maribel Fernández

  3. Inria Bordeaux Sud-Ouest, Inria, Talence, France

    Hélène Kirchner

  4. University of Bordeaux, CNRS UMR5800 LaBRI, Talence, France

    Bruno Pinaud

Authors
  1. Oana Andrei
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  2. Maribel Fernández
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  3. Hélène Kirchner
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  4. Bruno Pinaud
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Corresponding author

Correspondence to Bruno Pinaud .

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Editors and Affiliations

  1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA

    William S. Hlavacek

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Andrei, O., Fernández, M., Kirchner, H., Pinaud, B. (2019). Strategy-Driven Exploration for Rule-Based Models of Biochemical Systems with Porgy. In: Hlavacek, W. (eds) Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, vol 1945. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9102-0_3

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  • DOI: https://doi.org/10.1007/978-1-4939-9102-0_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9100-6

  • Online ISBN: 978-1-4939-9102-0

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