BioUML user interface

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BioUML workbench interface.
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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)

  • WebAction-tree-run workflow-icon.png Run workflow
  • WebAction-tree-open external url-icon.png Open external link
  • WebAction-tree-open diagram 2-icon.png Open diagram
  • WebAction-tree-open tree table-icon.png Open view
  • WebAction-tree-open genome browser-icon.png Open track
  • WebAction-tree-open sequence-icon.png Open sequence
  • WebAction-tree-open table-icon.png Open table
  • WebAction-tree-open text-icon.png Open text document
  • WebAction-tree-open optimization-icon.png Open optimization
  • WebAction-tree-open analysis-icon.png Open analysis
  • WebAction-tree-open script-icon.png Open script
  • WebAction-tree-open web-icon.png Open document
  • WebAction-tree-open image-icon.png Open image
  • WebAction-tree-open plot-icon.png Open plot
  • WebAction-tree-open structures-icon.png Open as table
  • WebAction-tree-download file-icon.png Download file
  • WebAction-tree-open chat-icon.png Start chat
  • WebAction-tree-open group chat-icon.png Group chat
  • WebAction-tree-open work-icon.png Edit work
  • WebAction-tree-expand-icon.png Expand/collapse
  • WebAction-tree-new element-icon.png New element
  • WebAction-tree-new script-icon.png New JS script
  • WebAction-tree-new r script-icon.png New R script
  • WebAction-tree-new workflow-icon.png New workflow
  • WebAction-tree-new diagram-icon.png New diagram
  • WebAction-tree-new work-icon.png New work
  • WebAction-tree-new folder-icon.png New folder
  • WebAction-tree-open new optimization-icon.png New optimization
  • WebAction-tree-view plot-icon.png View
  • WebAction-tree-import element-icon.png Import
  • WebAction-tree-export element-icon.png Export
  • WebAction-tree-save element as-icon.png Save a copy
  • WebAction-tree-save folder as-icon.png Copy folder
  • WebAction-tree-remove element-icon.png Remove
  • WebAction-tree-remove project-icon.png Remove project
  • WebAction-tree-find project-icon.png Find project

Database types

  • PublicDB icon.png Public database with read access
  • ProtectedDB R icon.png Protected database with read access enabled
  • PublicDB R icon.png Public database with read access, write access disabled
  • PublicDB W icon.png Public database with read access, write access enabled
  • PublicDB RW icon.png Public database with read and write access
  • LocalDB icon.png Local database
  • RemoteDB R icon.png Remote protected read-only database (no access)
  • RemoteDB RW icon.png Remote protected read-and-write database (no access)

Element types

Information box

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

Viewparts area

  • Edit description icon.png Edit
  • WebAction-toolbar-save document-icon.png Save
  • Add element icon.png Add a new element
  • Recalculate doc icon.png Recalculate the document
  • Search icon.png Start search
  • Discard icon.png Discard changes / clear elements
  • Execute icon.png Execute
  • Add2docpane icon.png Add/ apply to the item in the document pane
  • Add2newdia icon.png Add to a new diagram
  • Stop icon.png Stop (the selected tasks)
  • Accept2viewparts icon.png Accept the layout edited in the document pane to the viewparts area
  • WebAction-tree-remove element-icon.png Remove
  • Add2clipboard icon.png Add to clipboard
  • Insertin2dia icon.png Insert into the diagram

General control panel

Toolbar actions (web edition)

  • WebAction-toolbar-logout-icon.png Log-out
  • WebAction-toolbar-login-icon.png Log-in
  • WebAction-toolbar-home-icon.png Start page
  • WebAction-toolbar-home ge-icon.png Start page
  • WebAction-toolbar-toggle ui-icon.png Toggle UI mode
  • WebAction-toolbar-toggle repository-icon.png Toggle repository
  • WebAction-toolbar-account info-icon.png Account info
  • WebAction-toolbar-project properties-icon.png Project properties
  • WebAction-toolbar-help-icon.png Help

  • WebAction-toolbar-save document-icon.png Save document
  • WebAction-toolbar-save document as-icon.png Save a copy
  • WebAction-toolbar-revert-icon.png Revert to saved
  • WebAction-toolbar-export-icon.png Export
  • WebAction-toolbar-import document-icon.png Import

  • WebAction-toolbar-undo in-icon.png Undo in
  • WebAction-toolbar-redo in-icon.png Redo in

  • WebAction-toolbar-zoom out-icon.png Zoom out
  • WebAction-toolbar-zoom in-icon.png Zoom in
  • WebAction-toolbar-fit to screen-icon.png Fit to screen
  • WebAction-toolbar-run script-icon.png Run script
  • WebAction-toolbar-generate script-icon.png Generate script

  • WebAction-toolbar-set auto layout-icon.png Set auto layout
  • WebAction-toolbar-clear auto layout-icon.png Clear auto layout
  • WebAction-toolbar-edit view options-icon.png View options

  • WebAction-toolbar-semantic zoom out-icon.png Semantic zoom out
  • WebAction-toolbar-semantic zoom in-icon.png Semantic zoom in

  • WebAction-toolbar-semantic overview-icon.png Overview
  • WebAction-toolbar-semantic default-icon.png Default
  • WebAction-toolbar-semantic detailed-icon.png Detailed

  • WebAction-toolbar-page-backward-icon.png Page backward
  • WebAction-toolbar-page-forward-icon.png Page forward

  • WebAction-toolbar-open-as-track-icon.png Open as track

  • WebAction-toolbar-pf highlight-icon.png Highlight/dehighlight originally loaded nodes

Basic operations

For information about handling files within the repository pane see the page.

For information about working with tables in the document pane see the page.

For information about working with diagrams in the document pane see the page.

See also

Personal tools

BioUML platform
Analysis & Workflows
Collaborative research
Virtual biology