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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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Abstract

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.


Publication metadata

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

Publication type: Report

Publication status: Published

Series Title: School of Computing Science Technical Report Series

Year: 2006

Pages: 18

Print publication date: 01/05/2006

Source Publication Date: May 2006

Report Number: 962

Institution: School of Computing Science, University of Newcastle upon Tyne

Place Published: Newcastle upon Tyne

URL: http://www.cs.ncl.ac.uk/publications/trs/papers/962.pdf


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