Difference between revisions of "BioUML user interface"

Revision as of 15:19, 5 June 2013

BioUML web edition interface.

BioUML workbench interface.

In either version the platform has a WIMP graphical user interface.

Both in the BioUML workbench and BioUML web edition the following areas can be found (see the figures):

A — the tabbed repository pane, where you find a collection of Databases, the uploaded Data files and the available Analyses methods (under the corresponding tabs), organized in a hierarchical tree structure. Here you can also see a list of Users involved with the current project.

B — the document pane (aka main pane or workspace), which is the part of the window where contents of projects and databases are viewed and handled. There can be as many tabs in the pane as there are diagrams, workflows, tables etc. opened in the workbench at the moment.

C — the information box containing tabs for the property inspector, which displays information about the data file or analysis method selected in the navigation pane above, and the text search engine.

D — the viewparts area, providing a number of options under the different tabs in a context-dependent manner.

E — the general control panel, the topmost bar showing a context-dependent set of icons for the available operations.

F — the repository pane toolbar containing a set of icons for the available operations depending on the item selected in the tree structure of the navigation pane.

List of icons

Repository pane

Tree actions (web edition)

• Run workflow
• Open external link
• Open diagram
• Open view
• Open track
• Open sequence
• Open table
• Open text document
• Open optimization
• Open analysis
• Open script
• Open document
• Open image
• Open plot
• Open as table
• Download file
• Start chat
• Group chat
• Edit work
• Expand/collapse
• New element
• New JS script
• New R script
• New workflow
• New diagram
• New work
• New folder
• New optimization
• View
• Import
• Export
• Save a copy
• Copy folder
• Remove
• Remove project
• Find project

Database types

• Public database with read access
• Protected database with read access enabled
• Public database with read access, write access disabled
• Public database with read access, write access enabled
• Public database with read and write access
• Local database
• Remote protected read-only database (no access)
• Remote protected read-and-write database (no access)

Element types

• Diagram
• analysis
• collection of sequences
• file
• folder
• galaxy data source method
• galaxy method
• html
• image
• matrix
• matrix library
• module
• profile
• script
• sequence
• site model
• table
• text
• track
• tree-table

Information box

• View the information in a new window / browser tab
• Edit the element description displayed in the Info tab (only for users' own files; fields highlighted in pink are editable)
• Launch search for the entered term in the selected database

Viewparts area

• Edit
• Save
• Add a new element
• Start search
• Discard changes / clear elements
• Execute
• Add/ apply to the item in the document pane
• Add to a new diagram
• Stop (the selected tasks)
• Accept the layout edited in the document pane to the viewparts area
• Remove
• Add to clipboard
• Insert into the diagram

General control panel

Toolbar actions (web edition)

• Log-out
• Log-in
• Start page
• Start page
• Toggle UI mode
• Toggle repository
• Account info
• Project properties
• Help

• Save document
• Save a copy
• Revert to saved
• Export
• Import

• Undo in
• Redo in

• Zoom out
• Zoom in
• Fit to screen
• Run script
• Generate script

• Set auto layout
• Clear auto layout
• View options

• Semantic zoom out
• Semantic zoom in

• Overview
• Default
• Detailed

• Page backward
• Page forward

• Open as track

• Highlight/dehighlight originally loaded nodes

Basic operations

See also

• Perspectives