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The Database Navigator is created after you have connected to a database - it is your gateway to anything related to that connection.
If you disconnect or close the Database Navigator, all connection-related windows will close as well.
Although Database Workbench strives to create an user interface that's the same for all available database engines, there are, of course, differences between engines. Below is a screen shot from three Database Navigators, one for InterBase, one for Oracle and one for MySQL (version 4, so no Stored Procedures etc yet). You can see the differences between, for example, the availability of database objects and single or multiple schemas.
Three Database Navigators - all the same, but different a well
Object context menus are available in both tabs, but in the Navigator tab, the lists themselves have menus as well.
Next: The Navigator