Linking the topology of a complex network to its long-term behavior is a basic problem in network theory, which has been on the focus of many recent research publications. To obtain a suitable Boolean model for a biological system, one must analyze the initial model and compare it with other experimental evidence, and if necessary, make adjustments by changing the topology of the wiring diagram. However, our knowledge on how to link the topology of a network to its long-term behavior is very limited due to the complexity of the problem. Since the need to consider complex biological networks has become ever greater, develop both theoretical foundation and algorithms for model selection and analysis has been brought to the forefront of biological network study.