geWorkbench

Overview

geWorkbench supports the dynamic loading and unloading of individual components for analysis and visualization. The Component Configuartion Manager (CCM) lists each available component, provides descriptive and license information, and controls loading and unloading. The ability to customize the loaded components may be useful to those who intend only to use particular types of analysis. It may in some cases also increase the responsiveness of the application, as potentially fewer viewer components may need to respond to particular data events (new data set, marker set activation etc.).

In brief, components can be loaded by checking the box adjacent to their entry in the list, and hitting Apply. Components can be unloaded in the same way, by unchecking their box and applying the change.

As shipped, the CCM may appear as in the figure below, with only basic components configured. Individual components can be added by clicking on their check boxes.

Available Component List

The list of components includes the following column headings:

• On/Off - checking will select the component for loading. Unchecking the box will lead to the component being unloaded.
• Name: Component name
• Author - Component author or source of primary calculation code.
• Version - Component version
• Tutorial - Link to web-based tutorial/manual if available.
• Tool URL - Link to tool home page if available.

Component Dependencies

geWorkbench tracks component dependencies. Adding a particular component may also require that components it depends on be added, e.g. adding a particular analysis component may also require adding a particular viewer. These dependencies are all handled in the CCM. An example is shown in the following figure, where adding the Gene Ontology Analysis component also requires adding the Gene Ontology Viewer component.

After clicking "Proceed", all needed components are selected to be added.

If a component requires agreeing to a license, the license will also be displayed at this time, with the option to accept or reject it.

Controlling display of components

Display

Displayed components can be limited by the following menu choices:

• All
• Only Loaded
• Only Unloaded

Show by type

In addition, a pulldown menu allows only particular categories of components to be viewed:

• Analysis
• Filters
• Normalizers
• Visualizers
• Others - any components that fall in none of the above categories.

Keyword Search

The list of components can be searched by typing in a word here. Displayed choices will be progressively narrowed as typing occurs.

Controls

Once the desired changes to the list of components has been made, the changes are put into effect by pushing the Apply button.

• Apply - if any changes have been made to the check-boxes indicating which components are to be loaded, pushing "Apply" causes the changes to actually be be made.
• Reset - If changes have been made but "Apply" has not been pushed, set all checkboxes back to their previous state.
• Close - Close the CCM window.

• View license - If a license is required for a component, it can be displayed by highlighting the component in the list and pressing this button.