Figure 6

The multistate builder window, used to modify a multistate species. (a) Iconographic representation of a protein (called Cdh1) with ten phosphorylation sites, (b) Representation closer to MSMB’s encoding of the protein in (a): the species contains a single site (called P) with values ranging from 0 to 10; (c) Cdh1 protein can exist in several single states (i.e. specific values of the site P). The shape of the site represents the fact that different states can have different activity levels; (d) The multistate builder window that is used in MSMB to modify a multistate species. Information about the protein depicted in (a-c) is displayed. The interface devoted to modifying the sites structure is shown on the left. Current sites are listed in the lower part of the window. The user can select a site to modify, and its current state values will be loaded into the central part of the window. Once the changes are complete, the user can click the “Add/Change” button and the updated site will be listed. On the right, the interface devoted to the assignment of initial values for each state of the species is shown. If a species contains more than one site, all combinations of the different states of each site are generated and displayed, each with the initial quantity set as the default value for the species initial quantity. The user can specify a different initial value for the desired states. The “Update model” button saves all changes made to the model.