Modelling dynamic structures of biological systems with quantitative coloured Petri nets.

Biological systems often exhibit dynamic structures that generate numerous repeated or similar structures driven by fundamental evolutionary, biochemical, and systematic principles. These structures hinder the modelling and analysis of such systems due to their inherent complexity. To address this challenge, we propose a workflow for modelling and analysing dynamic structures of biological systems using quantitative coloured Petri nets (QPNC). The workflow describes a stepwise approach toward modelling and simulating dynamic and scalable structures of biological systems using three classes of coloured Petri nets, offering either deterministic, stochastic or hybrid semantics. We illustrate our protocol using the Gray-Scott system as a typical case study showing how two species react and diffuse over time and space, capturing typical biological patterns such as spots or stripes.