Coloured Petri nets for multi-level, multiscale, and multi-dimensional modelling of biological systems

Abstract

Due to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets have been successfully applied to multi-level, multiscale and multi-dimensional modelling of some biological systems, addressing many of these challenges. In this paper, we first review the basics of coloured Petri nets and some popular extensions, and then their applications for multi-level, multiscale and multi-dimensional modelling of biological systems. This understanding how to use coloured Petri nets for modelling biological systems will assist readers in selecting appropriate coloured Petri net classes for specific modelling circumstances.