Mathematical model is one of the most important methods to depict integrated qualitative, dynamic and topological behavior or activity of intracellular signal network, including diverse relationships between involved components. There are many computational modeling techniques applied for different purposes, such as Bayesian network, HMM (hidden Markov model), neural network etc. Mathematical models can be presented as many forms, including dynamic systems, differentiate equation, statistical model, or logical models. Although a model is initially for the topological representation of its components and their correlations, the description in the model of the biological system’s dynamic behavior enables its predictive power. The most important thing is to uncover and interpret those unexpected behavior encoded in the design of biological networks. A collection of models of the MAPK pathway are discussed in [57] from different facets of emphasis, such as dual phosphorylations, feedback loop. In general, a mathematical model usually represents a system as a set of variables and a set of equations that establish relationships between the variables.