Fig. 1

General layout of Model Explorer: The network view (1) shows a bipartite graph representation of the metabolic model, which is both zoomable and pannable. Reactions and species are represented with different shades of the same colour (reactions are bright and species are dark). If the reaction/species is active the base colour is green, and red if blocked. Endpoint species (those which are either not produced or not consumed) have a light blue outline, while the biomass (growth) reaction has a thick yellow outline. Connections between reactions and metabolites are represented with grey semitransparent arrows that have either one or two arrowheads depending on reversibility. Compartment contours are shown in orange, and all species that belong to a compartment must be localized within its contour. The command panel (2) contains a set of function menus and a Search tool, which can be used to find species and reactions by their name or id. When using neighbour view in the Command Panel, and hovering the cursor over a reaction/species or selecting it, the names of the reaction/species and a list of its properties, neighbours, ancestors or blocked module mates is shown in the text panel on the right (3)