Automatically Generated Model of a Metabolic Network

Simon Borger (borger@molgen.mpg.de)
Wolfram Liebermeister (lieberme@molgen.mpg.de)
Jannis Uhlendorf (uhlndorf@molgen.mpg.de)
Edda Klipp (klipp@molgen.mpg.de)

Max Planck Institute for Molecular Genetics, Berlin, Germany


Abstract

We demonstrate an approach to automatically generating kinetic models of metabolic networks. In a first step, the metabolic network is characterised by its stoichiometric structure. Then to each reaction a kinetic equation is associated describing the metabolic flux. For the kinetics we use a formula that is universally applicable to reactions with arbitrary numbers of substrates and products. Last, the kinetics of the reactions are assigned parameters. The resulting model in SBML format can be fed into standard simulation tools. The approach is applied to the sulphur-glutathione-pathway in Saccharomyces cerevisiae.

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Japanese Society for Bioinformatics