Some models of cellular physiological functions are formulated as ordinary differential equations that contain multiple systems of simultaneous nonlinear equations. Simulation of such a model described in a declarative representation format requires determination of equations to be simultaneously solved with specification of independent and parameter variables in the model. In this report, a method for extracting systems of simultaneous equations in a cell model is presented. The present method analyzes a graph representation of a model and extracts the subgraphs that represent equation systems to be simultaneously solved, by efficiently interactive selection of independent variables of the model. ©2009 IEEE.