Reaction graph, metabolic network

In practice, a gray-box model is developed in steps. One early step is to decide which variables and interactions to include. This is often done by the sketching of an interaction-graph. It must then be decided if a variable should be a state or a dependent variable, and how the interactions should be formulated. In the case of metabolic reactions, the expression forms for the reactions have often been characterized in in-vitro experiments. If this has been done, there are also often in-vitro estimates of the kinetic parameters. For enzymatic networks, however, such in-vitro studies are much more rare, and it is hence typically less known which expression to choose for the reaction rates, and what a good estimate for the kinetic parameters is. In any case, the standard method of combining reaction rates, r,-, and an interaction graph into a set of differential equations is to use the stoichiometric coefficients, Sij... 

The Estrada index is a molecular descriptor encoding information on complexity of molecular graphs and is also used to describe characteristic features of complex systems of physicochemical interest, such as reaction, metabolic, and protein-protein interaction networks. 

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