"Network Dynamics for Systems Biology"
Networks in biological systems form a complex graph structure in which dynamics is local. This applies to the dynamics of both graph node variables, such as concentrations, and graph link variables, such as evolving or cell-state-specific regulatory relationships. Unlike most models of physical systems, the forms of the equations commonly used to model cellular network dynamics are very diverse. This is due to diversity both in biological mechanisms, e.g. those associated with membership in metabolic, signaling, transcriptional or mechanical networks, and in the common modeling approaches to each mechanism. Plausible models for these networks can be classified according to (a) their network structure and (b) their choice of node dynamics for each major biological mechanism. Such a taxonomy can be important for example in representing signal transduction networks involving the interaction of protein complex and transcriptional regulation networks.