Appendix A. Menu guide

Appendix A. Menu guide
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This appendix covers all menu items in BASE, including submenus. You should use it as a map to easily find your way through the menus. Some menu items are referring to other section of the documentation, that holds more information. The list of menu items is organized after three different types,

Configurations

Settings
Configure	Menu choice	Comment
Appearance of web client	BASE → Preferences…	Section 6.2.4, “Preferences”
Contact information (your own)	BASE → Contact information…	Section 6.2.1, “Contact information”
Most recently used items	The tab Most recent under BASE → Preferences…	the section called “The Recent items tab”
Other information (your own)	BASE → Other information…	Useful information about yourself.
Password (your own)	BASE → Change password…	Section 6.2.3, “Changing password”
Plugin messages	The tab Plugins under BASE → Preferences…	the section called “The Plugins tab”
Server settings	Administrate → Server settings…	Currently no documentation.

Miscellaneous

Miscellaneous
Action	Menu choice	Comment
About the program	Help → About…	Useful information about the program.
BASE project information	Help → BASE project site…	The home page of the BASE project
Disk usage overview	Administrate → Disk usage	Disk usage of users, groups etc. Currently no other documentation.
Exit from the program	BASE → Logout…	You are logged out and redirected to the login page.
License information	Help → License…	The GNU GPL (General Public License)
Load your current permissions	BASE → Reload permissions	This updates the logged in user's permissions. See Section 7.1, “The permission system”
Report program defects	Help → Report a bug…	This is where you should turn if there are any defects in the program
Restart server/program	Administrate → Restart BASE…	Restarts the program. Requires everyone, that were logged in, to identify themselves again with username and password.

Items

Items (A-H, I-P, Q-Z)
Want to view…		Menu path	Comment
A-H	All items own by yourself	View → All items	Gives a complete overview of all your items.
	Annotation types	Administrate → Types → Annotation types	Chapter 11, Annotations
	Array batches	Array LIMS → Array batches	Chapter 16, Array LIMS
	Array designs	Array LIMS → Array designs	Chapter 16, Array LIMS
	Array slides	Array LIMS → Array slides	Chapter 16, Array LIMS
	Biomaterial lists	Biomaterial LIMS → Biomaterial lists	Chapter 17, Biomaterial
	Bioplates	Biomaterial LIMS → Bioplates	Chapter 17, Biomaterial
	Biosources	Biomaterial LIMS → Biosources	Chapter 17, Biomaterial
	Categories of annotation types	Administrate → Types → Annotation type categories	Chapter 11, Annotations
	Clients	Administrate → Clients
	Data file types	Administrate → Platforms → Data file types	Section 12.2, “Data file types”
	Experimental platforms	Administrate → Platforms → Experimental platforms	Section 12.1, “Platforms”
	Experiments	View → Experiments	Section 18.3, “Experiments”
	Extra value types	Administrate → Types → Extra value types
	Extracts	Biomaterial LIMS → Extracts	Chapter 17, Biomaterial
	Files and directories	View → Files	Chapter 8, File management
	File types	Administrate → Types → File types	Section 8.3, “File types”
	Formulas	View → Formulas
	Groups	Administrate → Groups	Section 24.2, “Groups administration”
	Hardware	Administrate → Hardware	Chapter 14, Hardware
	Hardware types	Administrate → Types → Hardware types
Helptexts	Administrate → Clients, use the Helptext tab when viewing a client.
Hybridizations	View → Hybridizations	Chapter 17, Biomaterial
I-P	Jobs	View → Jobs
	Labeled extracts	Biomaterial LIMS → Labeled extracts	Chapter 17, Biomaterial
	Labels	Biomaterial LIMS → Labels
	MIME types	Administrate → Types → MIME types
	Messages	View → Messages
	News	Administrate → News
	Plates	Array LIMS → Plates	Chapter 16, Array LIMS
	Plate geometries	Array LIMS → Plate geometries	Chapter 16, Array LIMS
	Plate mappings	Array LIMS → Plate mappings	Chapter 16, Array LIMS
	Plate types	Array LIMS → Plate types	Chapter 16, Array LIMS
	Plugins	Administrate → Plugins → Definitions	Chapter 22, Plug-ins
	Plugin configurations	Administrate → Plugins → Configurations	Section 22.4, “Plug-in configurations”
	Plugin types	Administrate → Plugins → Types	Chapter 22, Plug-ins
	Projects	View → Projects	Chapter 7, Projects and the permission system
	Protocols	Administrate → Protocols
	Protocol types	Administrate → Types → Protocol types
Q-Z	Quota	Administrate → Quota
	Quota types	Administrate → Types → Quota types	Section 24.4, “Disk space/quota”
	Raw bioassays	View → Raw bioassays	Section 18.2, “Raw bioassays”
	Removed items	View → Trashcan	Section 6.5, “Trashcan”
	Reporter lists	View → Reporter lists
	Reporter types	Administrate → Types → Reporter types
	Reporters	View → Reporters
	Samples	Biomaterial LIMS → Samples
	Scans	View → Scans	Section 18.1, “Scans and images”
	Sessions	View → Sessions
	Software	Administrate → Software	Chapter 15, Software
	Software types	Administrate → Types → Software types
	Users	Administrate → Users	Chapter 24, Account administration