The Toolbox is placed in the left side of the user interface of Biomedical Genomics Workbench below the Navigation Area. It can be seen as a Processes tab, a Toolbox tab and a Favorites tab.
The Toolbox can be hidden, so that the Navigation Area is enlarged:
View | Show/Hide Toolbox
This path gives you the choice to hide the Toolbox, or to selectively hide any of the tabs associated to the Toolbox.