Figure 7

Complex Builder wizard. (a) Iconographic representation of two species: a multistate species (called Net1) with eight phosphorylation sites, and a simple species (called Cdc14). (b) Net1 and Cdc14 protein form a complex only with a limited number of states of Net1 (i.e. not all possible phosphorylation states of Net1 can form a complex with Cdc14). In this case, only states where between 0 and 5 phosphorylation sites allow the complex formation. (c) Complex Builder wizard, the window that helps the user manage complex formation with multistate species. The window is divided into three parts: top, bottom, and central. The top is where the name of the complex may be specified, following the rules of generic species names, but the wizard allows the user to have the name picked (and maintained) by MSMB so that it reflects the components that are listed in the complex. At the bottom, the user can decide to add only the species complex to the model (default) or add as well the complexation and decomplexation reactions in the list of reactions. Those reactions have an elaborate syntax (involving the “transfer state” concept) so the user can let the tool handle their creation. The center right area is where the current composition of the complex is displayed. Each component can be deleted or, if of multistate kind, its tracking can be changed. The center left area is a list of available species of the model that can be added as components of the complex. Regular species are listed in the upper list, multistate species are listed in the lower list.