1. A computer-implemented method for integrated modeling and simulation of a biological process comprising a plurality of chemical substances, the method comprising: constructing, using a computer, a model of the biological process, 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, at least one subsystem formed by representing a plurality of blocks of the model as a single block in the constructed model; simulating, using the computer, the constructed model of the biological process, the simulating, accepting the constructed model of the biological process as input, and generating a dynamic behavior of the constructed model as output; and displaying one or more results of simulating the constructed model of the biological process to a user.