This is the actual running of shape, it will initialise objects and values which are calculated from the parameters that have been set - see the options with the suffix 'shape_'. It will establish the database output files and other initial conditions and then perform replicate simulations as appropriately defined. In essense this is the master wrapper function for all other functions. If you want to test/see SHAPE's default run then simply call this function after loading the library you'll see an experiment built under your root directory. It at least requires that defineSHAPE have been run, else this is going to fail.
Useful links