Topology, metabolic network modeling

Another two key concepts in metabolic engineering are metabolic pathway analysis and metabolic pathway modeling. The former is used for assessing inherent network properties in the complete biochemical reaction networks. It involves identification of the metabolic network structure (or pathway topology), quantification of the fluxes through the branches of the metabolic network, and identification of the control structures within the metabolic network. 

We may model complex systems by top-down or bottom-up approaches. In the top-down approach, we describe the components from the systemic behavior of the actual system. For example, from the flow balance analysis in a steady-state bacterium, we learn the input and output flows, topology of the network, and the rates of maty metabolic reactions. 

Models of pathways exist in many forms but most of these are static representations, not dynamic models of metabolism. They show the network topology of interconnected pathways of enzymes or signalling molecules, but they contain no dynamic information on reaction rates of diffusive encounters. The JWS-online database (http //jjj.biochem.sun.ac.za/database/index.html) on the other hand, is a web-based database containing over 90 dynamics models. Of these however, only a few are approaching what is desired. 

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