1. A system for integrated modeling, simulation and analysis of a biological system that includes processes that may be described by chemical reactions, the system comprising: a modeling component for constructing a model of the biological system; a simulation engine in communication with said modeling component, said simulation engine accepting as input the constructed model of the biological system and generating dynamic behavior of the constructed model as output; and an analysis environment in communication with said simulation engine and said modeling component, said analysis environment for analyzing aspects of the constructed model.