Metabolic network reconstruction and their topological analysis

This chapter focuses on the way to build a metabolic network and how to analyze its structure. The first part of this chapter describes the methods of the network model reconstruction from biochemical data found in specialized databases and/or literature. The second part deals with metabolic pathway analysis as a useful tool for better understanding the complex architecture of intracellular metabolism. The graph analysis and the stoichiometric network analysis are important approaches for understanding the network topology and consequently the function of metabolic networks. Among the methods presented, the Elementary Flux Modes analysis will be more detailed. Finally, we illustrate in this chapter an example of network reconstruction from heterotrophic plant cells metabolism and its topological analysis leading to a huge number of Elementary Flux Modes.