1. A computer-implemented method for integrated modeling and simulation of a biological process comprising a plurality of chemical substances, the method comprising: (a) constructing, using a suitably programmed computer, a model of the biological process, the constructed model being modified by user commands received through both a graphical user interface and a textual user interface that is separate from the graphical user interface, the constructed model having a layered hierarchy comprising a plurality of hierarchical levels, at least one hierarchical level formed by creating at least one subsystem in the constructed model, each subsystem formed by representing a plurality of blocks of the model as a single block in the constructed model; (b) presenting each hierarchical level in a separate window in the graphical user interface (c) simulating, using the suitably programmed computer, the constructed model of the biological process, the simulating accepting the constructed model of the biological process as input and generating dynamic behavior of the constructed model as output; (d) automatically refining, using the suitably programmed computer, the constructed model based on the simulation; and (e) displaying one or more results of simulating the constructed model of the biological process to a user.