Ontology Driven Simulation of Biochemical Pathways Using Hybrid Petri Nets

Glycans are known to change in the earliest stage of cell development in complex living organisms. Glycoproteins and glycolipids effect the abundance level of cell surface glycans. Thus, the study of production and consumption of glycoproteins and glycolipids are important. In this paper, we present the Glycomics Modeling pathway simulation environment (GlyMpse), an ontology driven simulation model utilizing domain ontologies such as GlycO, EnzyO and ReactO as well as modeling ontology DeMO (to generate simulation models of biochemical pathways). The model provides insight to glycobiologists about the behavior of glycan abundance level on cell surface over time. We also tested GlyMpse with N-Glycan biosynthesis pathway to achieve steady state approximation with kinetic parameters generated by a genetic algorithm, as a starting point. Index words: Simulation, Ontology, Biochemiacal Pathways, Michaelis-Menton Kinetics ONTOLOGY DRIVEN SIMULATION OF BIOCHEMICAL PATHWAYS USING HYBRID PETRI NETS