Workspace

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Workspaces and Projects

In the Project Folders component there is a top-level object called a workspace.


Project Folders Workspace.png

The workspace can contain one or more separate projects, and each project can contain opened data files and analysis results. An analogy might be that a workspace is like a drawer in a filing cabinet, and projects are individual folders in that drawer. Projects allow data to be grouped, for example by experiment. A project can contain many different types of data, for example microarray data, FASTA sequence files and graphical images. The workspace as a whole, with all its projects and data nodes, can be saved and restored. However, only one workspace can be open at one time.

All data must belong to a project.

Creating a new project

There are two ways to create a new project. First, select the Workspace node in the Project Folders component. Then, either

(1) In the top-level Menu, select File->New->Project.

File New Project.png

or,

(2) In the Project Folders component, right-click on the Workspace and select "New Project".


Project Folders Workspace New Project.png


Either way, the new Project is placed into the workspace:


Project Folders Project.png


Project Menu Options

Right-clicking on a Project node gives a menu with the following options


Project Folders Project Options.png


Open Files


Open PDB File from RCSB Protein Data Bank

If Open PDB File from RCSB Protein Data Bank is chosen, a dialog box appears.


Project Folders Project Open RCSB PDB.png


Type in the name of a PDB structure entry and it will be retrieved from the RCSB Protein Data Bank and loaded into geWorkbench.


Rename

A dialog box will appear in which to enter a new name for the project.


T ProjectFolder RenameProject.png


Remove

Selecting Remove will remove the project and all of its data nodes.


Project Data Node Menu Options

Right-clicking on a project data node will produce a popup menu with the following options:


Project Folders Data Node Right-Click Menu.png


Save

Save the currently selected data node. This is implemented for the following data types:

  • Microarray gene expression - data is saved using the geWorkbench ".exp" format, regardless of the original format. This allows saving e.g. a merged dataset, and/or any array and marker sets that may have been created.
  • FASTA - saved in FASTA format (.fasta).
  • PDB - saved in PDB format (.pdb).
  • Network - saved using the Adjacency Matrix "ADJ" format (.adj).

Rename

A dialog box will appear in which a new name can be entered.


T ProjectFolder RenameDataset2.png


Remove

The selected data node and any child data nodes it may have will be removed.

Workspaces

Saving a Workspace

Saving a workspace saves all of projects and data belonging to that workspace to a file on disk. The workspace can later be reloaded to resume work. However, workspaces in general may not be compatible across different versions of geWorkbench.


File Save Workspace.png


A dialog box will appear in which the location and file name to which to save the workspace can be chosen.


File Save Workspace Dialog.png

Creating a New Workspace

Only one workspace at a time can be loaded in geWorkbench. Creating a new workspace will destroy the existing workspace. For this reason, if you opt to create a new workspace, you will be prompted as to whether to save the existing workspace first.

A new workspace can only be created from the top level menu bar.


File New Workspace.png


Select File->New->Workspace.