Reactive models for biological regulatory networks

Abstract

A reactive model, as studied by D. Gabbay and his collaborators, can be regarded as a graph whose set of edges may be altered whenever one of them is crossed. In this paper we show how reactive models can describe biological regulatory networks and compare them to Boolean networks and piecewise-linear models, which are some of the most common kinds of models used nowadays. In particular, we show that, with respect to the identification of steady states, reactive Boolean networks lie between piecewise linear models and the usual, plain Boolean networks. We also show this ability is preserved by a suitable notion of bisimulation, and, therefore, by network minimisation.ERDF - The European Regional Development Fund through the Operational Programme for Competitiveness and Internationalisation - COMPETE 2020 Programme and by National Funds through the Portuguese funding agency, FCT - Fundação para a Ciência e a Tecnologia, within project POCI-01-0145-FEDER-030947. and project with reference UID/MAT/04106/2019 at CIDMA. D. Figueiredo also acknowledges the support given by FCT via the PhD scholarship PD/BD/114186/201