Abstract
This paper presents a hierarchical framework for modeling intracellular biological phenomena. In addition to describing material flow in biological systems, this approach also accounts for regulatory flow. Whereas material flows serve as inputs to be acted upon by the system, regulatory flows refer to cellular processes that serve to control the process response to material inputs. Unlike other models, this approach accounts for the explicit time delays present in both regulatory and material flows. Iterations between experimental and modeling work allows for efficient improvements in both experimental design and model structure.
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