Construction of elementary mode collections. (a) This scheme represents some of the elementary modes calculated between fumarate and 2-oxoglutarate in the citrate cycle pathway. Each color corresponds to a different elementary mode; numbers indicate the identifiers of elementary modes as in Additional data file 1, and doors represent start and end compounds of elementary modes. This figure illustrates the combinatorial nature of elementary modes: several of them are almost identical except for one or two reactions, and a given reaction can belong to several elementary modes. (b) The composition of the EM1 collection (left) and how elementary modes were merged to build the EM2 collection (right). Three independent sets from EM1 can be merged into two sets in EM2 if they share a common boundary compound.