Menu Bar

Revision as of 18:53, 14 February 2011 by Smith (talk | contribs) (Release and System Information)

Menu Bar

Introduction

The Menu Bar is located at the top of the geWorkbench graphical interface, and provides access to important actions, settings and information.

This section will briefly cover the individual menu items. Some items have their own more extensive documentation, and links to this will be provided.

Menu Bar.png


The first two items in the menu, "File" and "Edit", apply to the Project Folders component, described in the next section.

Background on the Project Folders component

In brief, the Project Folders component is used for data organization and management. It contains four types of "nodes", arranged in a hierarchical fashion.

  • Workspace - A workspace contains all the data for a geWorkbench session. Only one workspace can be present at a time. A workspace can be saved and reloaded. Workspaces are used to hold one or more projects.
  • Project - A project is used to hold the data and the analysis results for a particular experiment. A workspace can contain more than one project, and one can easily switch between projects.
  • Data nodes - These contain data either loaded from files on disk or retrieved from the network.
  • Result nodes - After an analysis is done in geWorkbench, a result node is created as a child of the data node from which it was created.


The following diagram shows the Project Folders component with a single data node and its child t-test analysis result node.


Menu Bar Project Folders.png


Further details about the Project Folders component can be found in the Projects section.

File

The following choices are available under the File menu.

Menu Bar File Open.png


Open

  • File - Open a specific data file from disk. A Project node must be selected in the Project Folders component. A standard file browser will appear, and the user can select from any of the file types that geWorkbench can directly load. The data file will be loaded into the selected project. If no project node yet exists, one must be created before a data file can be loaded.
  • Workspace - Open a previously saved geWorkbench workspace. A standard file browser will appear with which to locate the desired workspace file. As shown in the figure below, a dialog will appear warning the user that the current workspace will be overwritten. The user is offered the option to save the current workspace before proceeding. "Open Workspace" can be used regardless of what node is currently selected in the Project Folders component.


Menu Bar File Open Workspace Loading.png

Save

  • Workspace - Save the current geWorkbench workspace to a file on disk. All projects, data and result nodes will be saved.


Menu Bar File Save Workspace.png

New

  • Workspace - Create a new workspace in the Project Folders component. Doing so will destroy the existing workspace, so the user will be prompted as to whether to save the current workspace. This is shown in the following diagram.


Menu Bar File New Workspace Creation.png


  • Project - Within a workspace, create a new project. Any number of projects can be created in a workspace.

Export

  • Export the microarray dataset currently selected in the Project Folders component in the "Affymetrix Matrix File Format" (.exp). This format preserves array sets that may have been defined.

Merge Datasets

If more than one data file originating from the same platform has been loaded into a project, the datasets can be merged into one for analysis. See Local_Data_Files#Microrray_data_and_merging_datasets for further information.

Remove

This option will remove a project or a data node under the project from the Project Folders component. It will not remove a top-level workspace.


Exit

Close geWorkbench. The user will be prompted as to whether to save the workspace before closing.

Menu Bar Exit.png


Image Snapshot

Edit

Rename

  • Project - Rename the currently selected project. (Also works when a project child node is selected).
  • File - Rename the currently selected data or result node.

View

Clear Selection

Commands

Menu Bar Commands.png

Tools

Help

Menu Help.png


Help Topics

Online Help.png


Links to external sites

geWorkbench.org - This is the URL of the geWorkbench project home page. It contains full information about geWorkbench.

Knowledge Center - The National Cancer Institute's Molecular Analysis Tools Knowledge Center provides user support for geWorkbench.

Release and System Information

About - Displays the geWorkbench startup splash screen with developer credits.

Show Welcome Screen - The first time a new version of geWorkbench is started, this screen is displayed. This menu item will redisplay the welcome screen.

System Info - Displays information about the operating system, the Java version and Java memory usage.

Menu System Info.png


Version Info - Displays the version number of the currently running copy of geWorkbench.


Menu Bar Version Info.png