We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, translocation matrix, degradation matrix, and stochastic force. These four elements are balanced to determine the network dynamics, which gives arise to a special stochastic differential equation supplemented by a relationship between the stochastic force and the degradation matrix. Important network behaviors can be obtained from the potential function without explicitly solving for the time-dependent solution. The existence of such a potential function suggests a global optimization principle. The existence stochastic force corresponds naturally to the hierarchical structure in metabolic networks. We provide. theoretical evidences to justify our proposal by discussing its connections to others large-scale biochemical systems approaches, such as the network thermodynamics theory, biochemical systems theory, metabolic control analysis, and flux balance analysis. Experimental data displaying stochasticity which carries important biological information are also pointed out. (c) 2005 Elsevier Ltd. All rights reserved.