Searching for significant reactions and subprocesses in models of biological systems based on Petri nets

Abstract

The primary aim of this research was to propose algorithms enabling the identification of significant reactions and subprocesses within models of biological systems constructed using classical Petri nets. These solutions allow to performance of two analysis methods: an importance analysis for identifying individual reactions critical to the functioning of the model and an occurrence analysis for finding essential subprocesses. To demonstrate the utility of these methods, analyses of an example model have been performed. In this case, it was a model related to the DNA damage response mechanism. It is worth noting that the proposed analyses can be applied to any biological phenomenon represented using the Petri net formalism. The presented analysis methods represent an extension of classical Petri net-based analyses. Their utility lies in their potential to enhance our comprehension of the biological phenomena under investigation. Furthermore, they can lead to the development of more effective medical therapies, as they can aid in the identification of potential molecular targets for drugs.

Keywords: Biological systems; Importance analysis; Occurrence analysis; Petri net-based models; Significant reactions and subprocesses; t-invariants analysis.