Modeling Energy Producing Process in Lipid Metabolism by Using Work Flow Petri Nets

• Main Authors: Su Jen Lee, 李樹人
• Other Authors: 呂芳懌
• Format: Others
• Language: en_US
• Published: 2010
• Online Access: http://ndltd.ncl.edu.tw/handle/80310635950957725279

碩士 === 東海大學 === 資訊工程學系 === 98 === Motivation: To convey the hierarchical metabolic pathways knowledge to software engineers when developing biochemical applications is a frustrating chore for biochemists. Our goal is to provide a simple method to present the behavior of metabolic pathways in a graphical and dynamic ways, and hope that this method is acceptable and helpful to both biochemists and programmers. Petri Nets, as a formal dynamic model, have been widely used in the fields of computer science and biological processes to model systems. Computer networks and genetic network are two typical examples. Since the reactions in a metabolism are dynamic and variable, it is adequate to simulate these processes with Petri Nets. Therefore, in this study, we propose a Petri-Nets-based discrete event system, called Workflow Petri Nets (WF Nets for short), with which workflow control functions can be used to effectively model and simulate the regulation and cooperation of biochemical reactions in metabolic pathways. With the model, the biochemical properties of metabolic pathways in an organism can be presented concretely. The model can also be used as a educational system to tell students how metabolic pathways work or as a prediction tool to predict the possible biochemical reactions. Through the simulation researchers can realize the reason of a metabolic disease and even develop new drugs. Our methodology is mainly based on WF-Net, which is an extended version of typical Petri Nets, particularly suitable for modeling the control behavior of the conversions and interactions of metabolites in biochemical reactions.