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Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits

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Synthetic Gene Circuits

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2229))

Abstract

Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide direct insight into the relation between the feedback structure and the dynamical properties of a network. We review qualitative modeling approaches by focusing on two specific formalisms, Boolean networks and piecewise-linear differential equations, and illustrate their application by means of three well-known synthetic circuits. We describe various methods for the analysis of state transition graphs, discrete representations of the network dynamics that are generated in both modeling frameworks. We also briefly present the problem of controlling synthetic circuits, an emerging topic that could profit from the capacity of qualitative modeling approaches to rapidly scan a space of design alternatives.

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Acknowledgements

We would like to thank our friend and colleague Jean-Luc Gouzé, for a critical reading of the manuscript and many useful discussions. This work has been supported by the ANR projects Maximic (ANR-17-CE40-0024-01) and ICycle (ANR-16-CE33-0016-01), and Inria IPL CoSy.

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Authors and Affiliations

  1. Université Côte d’Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore Team, Sophia Antipolis, France

    Madalena Chaves

  2. Université Grenoble Alpes, Inria, Grenoble, Montbonnot, Saint Ismier Cedex, France

    Hidde de Jong

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Correspondence to Hidde de Jong .

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  1. School of Engineering, Institute for Bioengineering, University of Edinburgh, Edinburgh, UK

    Filippo Menolascina

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Chaves, M., de Jong, H. (2021). Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits. In: Menolascina, F. (eds) Synthetic Gene Circuits . Methods in Molecular Biology, vol 2229. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1032-9_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1032-9_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1031-2

  • Online ISBN: 978-1-0716-1032-9

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