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A Case for Using Signal Transition Graphs for Analysing and Refining Genetic Networks

Lookup NU author(s): Richard Banks, Dr Victor Khomenko, Dr Jason Steggles



In order to understand and analyse {\it genetic regulatory networks}, the complex control structures which regulate cellular systems, well supported qualitative formal modelling techniques are required. In this paper we make a case that biological systems with deterministic behaviour can be modelled by speed-independent circuits. We apply techniques from asynchronous circuit design, based on {\it Signal Transition Graphs (STGs)}, to modelling, visualising and analysing genetic regulatory networks. STGs are an interpreted Petri net model that have been extensively used in asynchronous circuit design. We investigate how the sufficient conditions ensuring that an STG can be implemented by a speed-independent circuit can be interpreted in the context of genetic regulatory networks.We observe that these properties provide important insights into a model and highlight areas which need to be refined. Thus, STGs provide a well supported formal framework for genetic regulatory networks that allows realistic models to be incrementally developed and analysed. We demonstrate the proposed STG approach with a case study of constructing and analysing a speed-independent circuit specification for lysis-lysogeny switch in phage lambda.

Publication metadata

Author(s): Banks R, Khomenko V, Steggles J

Publication type: Report

Publication status: Published

Series Title: School of Computing Science Technical Report Series

Year: 2008

Pages: 21

Print publication date: 01/04/2008

Source Publication Date: April 2008

Report Number: 1086

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

Place Published: Newcastle upon Tyne