Repository pane
Repository pane (or navigation pane, or simply tree) is the user interface element which present both in BioUML workbench and BioUML web edition in left-top part. It represents hierarchical structure of BioUML repository. Depending on BioUML installation and current perspective it may include several tabs, each of them containing the tree of collections and elements. Predefined databases, user data, analysis methods and many more can be found in this tree. When you select an element by single mouse click, an information about this element is displayed in the information box and repository pane toolbar is updated reflecting context actions available for given element. The same context actions are available upon right mouse click. When you double-click on tree element, default action will be executed like opening of a document.
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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.
To expand an item
- 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
- 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, the file name 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 information 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 
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.
