Connections between subsystems in the SEED. The network of interactions that occur among 65 subsystems in the SEED used to regenerate the S. aureus model. Each box represents a subsystem. Colors correspond to the categories of metabolism described by the 2003 International Union of Biochemistry and Molecular Biology Metabolic Pathways chart (Sigma-Aldrich, http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/Metabolomics/Key_Resources/Metabolic_Pathways.html). Carbohydrates, green; amino acids, red; lipids, light blue; purines and pyrimidines, purple; and vitamins, coenzymes and hormones, gray. Abbreviations within subsystem boxes are explained in Additional File 2.