Example yeast network. One flux distribution for the central metabolic and amino acid biosynthesis pathways of yeast. Metabolite abbreviations, reaction details, and the symbolic flux relations used to calculate this steady state are provided in additional file 2: yeast_example.pdf. The values of the independent flux variables substituted into the flux relations are set in italic font. The mitochondrial compartment is separated with a purple boarder and all inter-compartmental transport reactions are given as orange arrows. Amino acid synthesis reactions are green, and all transport fluxes out of the system are depicted with green cartoon bubbles. The pentose phosphate pathway reactions are given in red and the urea cycle is shown in brown. Dots are placed next to reactions that are coupled; pink dots indicate the transformation of glutamate to oxoglutarate, and the blue dot shows the transformation of glutamine to glutamate. Species that occur in more than one place within one compartment are circled with a dotted blue line.