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

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. © 2008 University of Newcastle upon Tyne. Printed and published by the University of Newcastle upon Tyne, Computing Science, Claremont Tower, Claremont Road, Newcastle upon Tyne, NE1 7RU, England. Bibliographical details BANKS, R., KHOMENKO, V., STEGGLES, J. An analysis of the dynamics of British academic science [By] R.Banks, V.Khomenko and J.Steggles. Newcastle upon Tyne: University of Newcastle upon Tyne: Computing Science, 2008. (University of Newcastle upon Tyne, Computing Science, Technical Report Series, No. CS-TR-1086)