Petri nets: an introduction
Model checking
Signal Graphs: From Self-Timed to Timed Ones
International Workshop on Timed Petri Nets
SYNTHESIS OF SELF-TIMED VLSI CIRCUITS FROM GRAPH-THEORETIC SPECIFICATIONS
SYNTHESIS OF SELF-TIMED VLSI CIRCUITS FROM GRAPH-THEORETIC SPECIFICATIONS
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology)
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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 @l.