Appendix A. Menu guide

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,


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


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


Items (A-H, I-P, Q-Z)
Want to view… Menu path Comment
A-H All items own by yourself ViewAll items Gives a complete overview of all your items.
Annotation types AdministrateTypesAnnotation types Chapter 11, Annotations
Array batches Array LIMSArray batches Chapter 16, Array LIMS
Array designs Array LIMSArray designs Chapter 16, Array LIMS
Array slides Array LIMSArray slides Chapter 16, Array LIMS
Biomaterial lists Biomaterial LIMSBiomaterial lists Chapter 17, Biomaterial
Bioplates Biomaterial LIMSBioplates Chapter 17, Biomaterial
Biosources Biomaterial LIMSBiosources Chapter 17, Biomaterial
Categories of annotation types AdministrateTypesAnnotation type categories Chapter 11, Annotations
Clients AdministrateClients  
Data file types AdministratePlatformsData file types Section 12.2, “Data file types”
Experimental platforms AdministratePlatformsExperimental platforms Section 12.1, “Platforms”
Experiments ViewExperiments Section 18.3, “Experiments”
Extra value types AdministrateTypesExtra value types  
Extracts Biomaterial LIMSExtracts Chapter 17, Biomaterial
Files and directories ViewFiles Chapter 8, File management
File types AdministrateTypesFile types Section 8.3, “File types”
Formulas ViewFormulas  
Groups AdministrateGroups Section 24.2, “Groups administration”
Hardware AdministrateHardware Chapter 14, Hardware
Hardware types AdministrateTypesHardware types  
Helptexts AdministrateClients, use the Helptext tab when viewing a client.    
Hybridizations ViewHybridizations Chapter 17, Biomaterial  
I-P Jobs ViewJobs  
Labeled extracts Biomaterial LIMSLabeled extracts Chapter 17, Biomaterial
Labels Biomaterial LIMSLabels  
MIME types AdministrateTypesMIME types  
Messages ViewMessages  
News AdministrateNews  
Plates Array LIMSPlates Chapter 16, Array LIMS
Plate geometries Array LIMSPlate geometries Chapter 16, Array LIMS
Plate mappings Array LIMSPlate mappings Chapter 16, Array LIMS
Plate types Array LIMSPlate types Chapter 16, Array LIMS
Plugins AdministratePluginsDefinitions Chapter 22, Plug-ins
Plugin configurations AdministratePluginsConfigurations Section 22.4, “Plug-in configurations”
Plugin types AdministratePluginsTypes Chapter 22, Plug-ins
Projects ViewProjects Chapter 7, Projects and the permission system
Protocols AdministrateProtocols  
Protocol types AdministrateTypesProtocol types  
Q-Z Quota AdministrateQuota  
Quota types AdministrateTypesQuota types Section 24.4, “Disk space/quota”
Raw bioassays ViewRaw bioassays Section 18.2, “Raw bioassays”
Removed items ViewTrashcan Section 6.5, “Trashcan”
Reporter lists ViewReporter lists  
Reporter types AdministrateTypesReporter types  
Reporters ViewReporters  
Samples Biomaterial LIMSSamples  
Scans ViewScans Section 18.1, “Scans and images”
Sessions ViewSessions  
Software AdministrateSoftware Chapter 15, Software
Software types AdministrateTypesSoftware types  
Users AdministrateUsers Chapter 24, Account administration