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 LJ
Editor(s)
Publication type Conference Proceedings (inc. Abstract)
Conference NameElectronic Notes in Theoretical Computer Science: Second International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC)
Conference LocationIasi, Romania
Year of Conference2009
Legacy Date3-4 September 2008
Volume227
Pages3-19
ISBN15710661
Full text is available for this publication:
In order to understand and analyse genetic regulatory networks (GRNs), 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 can be qualitatively modelled by speed-independent circuits. We apply techniques from asynchronous circuit design, based on Signal Transition Graphs (STGs), to modelling, visualising and analysing GRNs. STGs are a Petri net based model that has 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 GRNs. 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 GRNs 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 the lysis-lysogeny switch in phage λ.
PublisherElsevier B.V.
URLhttp://dx.doi.org/10.1016/j.entcs.2008.12.101
DOI10.1016/j.entcs.2008.12.101
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