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

  • Oana Andrei
  • Maribel Fernández
  • Hélène Kirchner
  • Bruno PinaudEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Computational systems biology Biochemical networks Rule-based modelling Graph transformations Strategic rewriting Visual Analytics Software 

Notes

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.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Oana Andrei
    • 1
  • Maribel Fernández
    • 2
  • Hélène Kirchner
    • 3
  • Bruno Pinaud
    • 4
    Email author
  1. 1.School of Computing ScienceUniversity of GlasgowGlasgowUK
  2. 2.Department of InformaticsKing’s College LondonLondonUK
  3. 3.Inria Bordeaux Sud-OuestInriaTalenceFrance
  4. 4.University of BordeauxCNRS UMR5800 LaBRITalenceFrance

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