Difference between revisions of "BioUML user interface"

Latest revision as of 13:09, 19 June 2013

BioUML web edition interface.

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.

[edit] List of icons

[edit] Repository pane

[edit] 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

[edit] 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)

[edit] Element types

[edit] 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

[edit] Viewparts area

Edit
Save
Add a new element
Recalculate the document
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

[edit] General control panel

[edit] 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

[edit] 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.

[edit] See also

@@ Line 44: / Line 44: @@
 ===Viewparts area===
-*[[File:Edit_description_icon.png|20px]] Edit
+*[[File:Edit_description_icon.png]] Edit
 *[[File:WebAction-toolbar-save_document-icon.png]] Save
 *[[File:Add_element_icon.png]] Add a new element
+*[[File:Recalculate_doc_icon.png]] Recalculate the document
 *[[File:Search icon.png]] Start search
 *[[File:Discard_icon.png]] Discard changes / clear elements
-*[[File:Execute_icon.png|20px]] Execute
+*[[File:Execute_icon.png]] Execute
-*[[File:Add2docpane_icon.png|20px]] Add/ apply to the item in the document pane
+*[[File:Add2docpane_icon.png]] Add/ apply to the item in the document pane
 *[[File:Add2newdia_icon.png]] Add to a new diagram
-*[[File:Stop_icon.png|20px]] Stop (the selected tasks)
+*[[File:Stop_icon.png]] Stop (the selected tasks)
-*[[File:Accept2viewparts_icon.png|20px]] Accept the layout edited in the document pane to the viewparts area
+*[[File:Accept2viewparts_icon.png]] Accept the layout edited in the document pane to the viewparts area
 *[[File:WebAction-tree-remove_element-icon.png]] Remove
-*[[File:Add2clipboard_icon.png|20px]] Add to clipboard
+*[[File:Add2clipboard_icon.png]] Add to clipboard
-*[[File:Insertin2dia_icon.png|20px]] Insert into the diagram
+*[[File:Insertin2dia_icon.png]] Insert into the diagram
 ===General control panel===
@@ Line 64: / Line 65: @@
 ==Basic operations==
-===Navigating the file tree===
-Menu items containing one or more files (file collections) can be expanded/collapsed to show/hide their sublevels. Any such item, like a database, a folder, a track or a matrix library, has a white horizontal arrowhead to the left of its icon and name in the file tree area.
+For information about '''handling files''' within the repository pane [[Repository pane|see the page]].
-To expand an item
+For information about working with '''tables''' in the [[document pane]] [[Table document|see the page]].
-*click on the white arrowhead (the arrowhead will become black and downward),or
-*click on the item name and then on the '''Expand/collapse''' icon in the [[repository pane toolbar]] above, or
-*right-click on the item and select the '''Expand/collapse''' option from the context menu.
-To collapse an item
+For information about working with '''diagrams''' in the [[document pane]] [[Diagram document|see the page]].
-*click on the black downward arrowhead next to the icon and name of the expanded item, or
-*click on the item name and then on the '''Expand/collapse''' icon in the [[repository pane toolbar]] above, or
-*right-click on the item and select the '''Expand/collapse''' option from the context menu
-If the menu expands beyond the current visible area, use the horizontal and vertical scrollbars.
-===Handling files===
-When the mouse pointer hovers over a file name, it will gain a faint-bluish background.
-Upon a single click on a file name, its background will turn into a persistent light blue, and '''information about this file''' will be displayed in the property inspector tab of the Info Box.
-Double-clicking on a file name will '''open''' it under a new tab in the document pane, and the file name will be emphasized in bold as long as the corresponding tab is in the document pane’s foreground. Only files with an icon attached can be opened this way.
-Files can also be opened by:
-*clicking on the file name and pressing the '''Open...''' icon in the [[repository pane toolbar]], or
-*right-clicking on the file name and selecting the '''Open...''' option from the context menu.
-Similarly, you can '''delete''' chosen files by clicking on the '''Remove''' option in the [[repository pane toolbar]] or the context menu.
-Most files can be '''exported'''. When the function is activated, a selection of different formats is provided for the export file to be generated. It is also available through the icon [[File:WebAction-tree-export_element-icon.png]] in the [[repository pane toolbar]]
-While the Open, Remove and Export options are present and work for nearly any file, the rest of the available operations is different among distinct file types.
-===Selecting input files===
-All analysis tools, and likewise all prepared workflows, require input data from a file in the [[repository pane]]. The respective file can be loaded into an analysis tool
-*by simple drag-and-drop of the file from the repository area into the corresponding field in the document pane, or
-*by clicking into this field and making the selection from the directory which opens.
-Multiple selections can be done only in the second way.
 ==See also==
 *[[Perspective]]s
+*[[Features]]
 [[Category:User interface]]

Difference between revisions of "BioUML user interface"

Latest revision as of 13:09, 19 June 2013

Contents

[edit] List of icons

[edit] Repository pane

[edit] Tree actions (web edition)

[edit] Database types

[edit] Element types

[edit] Information box

[edit] Viewparts area

[edit] General control panel

[edit] Toolbar actions (web edition)

[edit] Basic operations

[edit] See also

Personal tools

Namespaces

Variants

Views

Actions

Search

BioUML platform

Community

Modelling

Analysis & Workflows

Collaborative research

Development

Virtual biology

Wiki

Toolbox