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Book Sections Year : 2021

Qualitative modeling, analysis, and control of synthetic regulatory circuits

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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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Dates and versions

hal-03094873 , version 1 (04-01-2021)

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Madalena Chaves, Hidde de Jong. Qualitative modeling, analysis, and control of synthetic regulatory circuits. Filippo Menolascina. Synthetic Gene Circuits: Methods and Protocols, 2229, Humana Press, pp.1-40, 2021, Methods in Molecular Biology, ⟨10.1007/978-1-0716-1032-9_1⟩. ⟨hal-03094873⟩
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