In recent years the number of sequenced and annotated plant genomes has increased significantly, and novel approaches are required to retrieve valuable information from these data sets. The field of systems biology has accelerated the simulation and prediction of phenotypes derived from specific genotypic modifications under defined growth conditions. The biochemical potential of a cell from a specific plant tissue (e.g., seed endosperm) can be derived from its genome in the form of a mathematical model by the method of metabolic network reconstruction. This model can be further analyzed by studying its network properties, analyzing feasible pathway routes through the network, or simulating possible flux distributions of the network. Here, we describe two approaches for identification of all feasible routes through the network (elementary mode analysis) and for simulation of flux distribution in the network based on plant physiological uptake and excretion rates (flux balance analysis). © 2014 Springer Science+Business Media, New York.