Connected scenarios across multiple subsystems. (A) Subsystems in the SEED are depicted as colored boxes and the connections between the subsystems are shown as arrows. Directionality of the arrows shows the flow of output compounds from scenarios in one subsystem that are used as input compounds for scenarios in another subsystem. Four connections between subsystems are expanded to display the scenario within one subsystem that is connected to a scenario in a different subsystem. In this case, a set of subsystems and scenarios is depicted that represents the conversion of glucose into the amino acid tyrosine. (B) We have developed a tool to find paths through connected scenarios across multiple subsystems. The table shows the initial input compound, target output compound and the necessary scenarios to complete the conversion. Each scenario is treated as a "higher-order" reaction by the tool. Output from the tool shows which scenarios were used, which main compounds were used, and the stoichiometry of the overall inputs and outputs necessary to convert the input compound to the output compound.
DeJongh et al. BMC Bioinformatics 2007 8:139 doi:10.1186/1471-2105-8-139