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If you regularly plan on creating a backup for a certain database, use the Backup and Restore nodes in the Enterprise Manager. These will use backup and restore projects, saved to a file, so you can re-use them at a later time.
For a quick backup, simply use the Backup Database node in the Database Navigator or from the context menu for a database in the Enterprise Manager via Administration & Maintenance | Backup Database. Both options will show the dialog below:
The Backup Database Dialog
Click OK to start the backup, this might take a while and Database Workbench will be unavailable while waiting for MySQL to finish the backup.
An explanation of the options: