Classical Petri net has been applied into biological analysis, especially as a qualitative model for biochemical pathways analysis, but lack of the ability for quantitative kinetic simulations. In our study, we presented an integra- tion work of the qualitative model--Petri nets with the quantitative approach-ordinary differential equations （ODEs） for the modeling and analysis of metabolic networks. As an application of our study, the computational modeling of arachidonic acid （AA） biochemical network was provided. A Petri net was set up to present the constraint-based dynamic simulations on AA metabolic network combined with the validated ODEs model. Furthermore, Graphics Processing Unit （GPU） was adopted to accelerate the calculation of kinetic parameters unavailable from experi- ments. Our results have indicated that the proposed simulation method was practicable and useful with GPU accel- eration, and provides new clues for the large-scale qualitative and quantitative models of biochemical networks.
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