JWS-online

JWS Online. [197] A tool for simulation of kinetic models from a curated database http //www.jjj.bio.vu.nl/... 

Very often a mixture of these two approaches is used to determine the values of the parameters. Good examples are Dano et al. [78] and Chassagnole et al. [79]. In these studies many parameters were taken from the literature and, in a parameter estimation approach, were allowed to vary within experimental error to fit the unknown parameters. When considering dynamics, the boundary conditions of the network have to be supplied as explicit functions of time, and therefore they have to be measured in order to give good values for parameter with parameter estimation [74, 79]. Many detailed and core models can be interrogated online at JWS online (www.jjj.bio.vu.nl) [80]. 

Olivier, B. G. Snoep, J. L. Web-based kinetic modelling using JWS Online. Bioinformatics 2004, 20 2143-2144. 

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. 

Steed JW, Atwood JL Supramolecular chemistry, 2009, John Wiley and Sons, online text. ISBN 0470740892, 9780470740897. 

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