Novel techniques for acquiring metabolomics data continue to emerge. Such data require proper storage in suitably configured databases, which then permit one to establish the size of microbial metabolomes (hundreds of major metabolites) and allow the nature, organisation and control of metabolic networks to be investigated. A variety of algorithms for metabolic network reconstruction coupled to suitable modelling algorithms are the ground substances for the development of metabolic network and systems biology. Even qualitative models of metabolic networks, when subject to stoichiometric constraints, can prove highly informative, and are the first step to the quantitative models, which alone can allow the true representation of complex biochemical systems.