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Modelling and simulating reaction-diffusion systems using coloured Petri nets
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DOI：10.1016/j.compbiomed.2014.07.004.png)
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Reaction-diffusion systems often play an important role in systems biology when developmental processes are involved. Traditional methods of modelling and simulating such systems require substantial prior knowledge of mathematics and/or simulation algorithms. Such skills may impose a challenge for biologists, when they are not equally well-trained in mathematics and computer science. Coloured Petri nets as a high-level and graphical language offer an attractive alternative, which is easily approachable. In this paper, we investigate a coloured Petri net framework integrating deterministic, stochastic and hybrid modelling formalisms and corresponding simulation algorithms for the modelling and simulation of reaction-diffusion processes that may be closely coupled with signalling pathways, metabolic reactions and/or gene expression. Such systems often manifest multiscaleness in time, space and/or concentration. We introduce our approach by means of some basic diffusion scenarios, and test it against an established case study, the Brusselator model. (C) 2014 Elsevier Ltd. All rights reserved.
Keyword:
Reaction-diffusion systems
Petri net framework
Coloured stochastic/continous/hybrid
Petri nets
Multiscaleness
Brusselator
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