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Modelling and analysing genetic networks: From Boolean networks to Petri nets

Lookup NU author(s): Dr Jason Steggles, Richard Banks, Professor Anil Wipat


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In order to understand complex genetic regulatory networks researchers require automated formal modelling techniques that provide appropriate analysis tools. In this paper we propose a new qualitative model for genetic regulatory networks based on Petri nets and detail a process for automatically constructing these models using logic minimization. We take as our starting point the Boolean network approach in which regulatory entities are viewed abstractly as binary switches. The idea is to extract terms representing a Boolean network using logic minimization and to then directly translate these terms into appropriate Petri net control structures. The resulting compact Petri net model addresses a number of shortcomings associated with Boolean networks and is particularly suited to analysis using the wide range of Petri net tools. We demonstrate our approach by presenting a detailed case study in which the genetic regulatory network underlying the nutritional stress response in Escherichia coli is modelled and analysed. © Springer-Verlag Berlin Heidelberg 2006.

Publication metadata

Author(s): Steggles LJ, Banks R, Wipat A

Editor(s): Priami, C

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Computational Methods in Systems Biology: International Conference (CMSB 2006)

Year of Conference: 2006

Pages: 127-141

ISSN: 0302-9743 (Print) 1611-3349 (Online)

Publisher: Springer-Verlag


DOI: 10.1007/11885191_9

Library holdings: Search Newcastle University Library for this item

Series Title: Lecture Notes in Computer Science

ISBN: 3540461663