Biological Metabolic Network Modeling Based On Petri Nets

Metabolism research is the basic field of life science. During years of metabolism study, a lot of metabolic experimental data have been acquired. And biochemical models derived from these data have been setup. However, there is a drawback in the traditional modeling method that is based on dynamic parameters because dynamic parameters are hard or even impossible to gain. So its application is limited. With the rapid development of Systems Biology, new method for metabolic network modeling emerges. Systems Biology is the synergistic application of experiment, theory and modeling.Based on Systems Biology methodology, the thesis introduced Petri Nets that prevail in system engineering to model metabolism. The description of Petri Net metabolic model was presented. And the analyze theory of Petri Net such as boundedness, S Invariant, T Invariant and optimization was discussed to simulate the model.Then we developed a package of Systems Biology software for Petri Net modeling on Visual C++ .NET, which enables us to construct and simulate Petri Net metabolic model on computer. The software system includes model editing module, model computing module and extended module. The former two modules constitute an integrated environment for model edit and simulate. The extended module accomplished PNML standardization of Petri Net model.Finally we established anaerobic metabolic, aerobic metabolic, and anaerobic-aerobic metabolic Petri Net models deriving from their biochemical reaction equations in the software we developed. Based on the Petri Net analyze method, we simulated these models with changing the input parameters of Glucose and Oxygen. The ATP generation curve of the simulation is consistent with biochemical theory. The result exhibits the correctness of Petri Net metabolic model and the promising future to employ Petri Net in metabolic modeling.