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 to create a constructed model, the constructed model having: a layered hierarchy of systems comprising a plurality of hierarchical levels, and at least one hierarchical level that comprises a subsystem in the constructed model, the 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.