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Updated: Feb 8, 2026

Micro-scale Engineering for Cell Biology
Published on: October 1, 2007
Coloured Hybrid Petri Nets: An adaptable modelling approach for multi-scale biological networks
Mostafa Herajy1, Fei Liu2, Christian Rohr3
1Department of Mathematics and Computer Science, Faculty of Science, Port Said University, 42521 Port Said, Egypt.
Abstract:
Coloured Petri nets are an excellent choice for exploring large biological models, particularly when there are repetitions of components. Such models can be easily adapted by slight modifications of parameter values related to colours. Similarly, multi-scale models could involve multiple spatial scales in addition to multiple time scales. Thus, they require the full interplay between stochastic as well as deterministic processes. In this paper we take these two aspects into account and present a modelling and simulation approach for multi-scale biochemical networks using Coloured Generalised Hybrid Petri Nets (GHPNC). GHPNC are a Petri net class that associates colours to Generalised Hybrid Petri Nets (GHPN), which incorporate discrete and continuous places in addition to stochastic and continuous transitions. Moreover, we present two case studies to illustrate typical applications taking advantage of such a Petri net class.
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