Validation and Analysis of Metabolic Pathways Using Petri Nets

Petri nets (PNs) have been widely utilized for modelling and analysing different expert systems which are characterized by concurrency, parallelism and conflicts. Due to the complex and dense nature of metabolic networks, modelling of these systems is needed to understand their topology. Petri net is one of the extensively used mathematical tools for modelling and studying metabolic pathways. Here, we have explained how analysis techniques of PNs can be exploited to simulate, validate and study the behaviour of metabolic pathways. We considered the biosynthesis of polyhydroxyalkanoates (PHAs) in the presence of krebs cycle for illustration to explain the validation and analysis process using Petri net. PHAs are synthesized by bacteria during nutrient lack conditions and are stored as energy storage materials. Krebs cycle is the competing pathway when glucose is the main source of carbon in PHA biosynthesis. The obtained results provide a valid mathematical model for confirming some of the known properties about their metabolic pathway and also provide some results on how the system will behave in the presence of krebs cycle. The model can be used in further studies to get new insights in this pathway along with other competing pathways. Analysis of the metabolic pathways can be more useful if this Petri net approach is related with some experimental approach.