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

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  2. Richard Banks
  3. Dr Victor Khomenko
  4. Dr Jason Steggles
Author(s)Banks R, Khomenko V, Steggles J
Publication type Report
Series TitleSchool of Computing Science Technical Report Series
Year2008
DateApril 2008
Report Number1086
Pages21
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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.
InstitutionSchool of Computing Science, University of Newcastle upon Tyne
Place PublishedNewcastle upon Tyne
URLhttp://www.cs.ncl.ac.uk/publications/trs/papers/1086.pdf
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