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geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization, and annotation of biomedical data. Many kinds of analysis are supported.  For microarrays, there are tools for filtering and normalization, basic statistical analyses, clustering, network reverse engineering, as well as many common visualization tools. For sequence data, there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis. geWorkbench provides access to a variety of external data sources, including microarray gene expression repositories (caArray), BLAST, gene annotation pages (via caBIO),protein and DNA sequence retrieval, and pathway diagrams (BioCarta), as well as acting a gateway to several computational services currently hosted on Columbia servers and clusters, including Pattern Discovery, Pudge (protein structure modeling), and SkyBase (database of molecular models).

Logging In

When you launch geWorkbench from GenomeSpace, you will se the Launch geWorkbench dialog.

If you have installed geWorkbench in the default location previously, click OK.  This will launch geWorkbench.

If you have never used geWorkbench before, or have not used the current version of geWorkbench, you need to install it.

Installing geWorkbench

If you have never used geWorkbench before, you can use the prompt you receive when you launch it from GenomeSpace to install it.  If you have used it and installed it in a non-standard directory, you can point GenomeSpace to that location in the prompt dialog.

To install geWorkbench:

  1. Click the link in the "please click here to install it" line and you will be taken to a page of installers. 
  2. Select and download the appropriate installer for your machine.
  3. Expand the ZIP archive containing the installer.
  4. Run the installer and go through the installation wizard.  It is recommended that you install geWorkbench in the default location; if you do not, you will have to enter the nonstandard location path in the prompt window every time you launch the tool.
  5. Go back to the prompt dialog and click OK. This should complete the launch of geWorkbench you began in GenomeSpace.

Enabling GenomeSpace Within geWorkbench

To access GenomeSpace in geWorkbench, enable the GenomeSpace component using the Component Configuration Manager.

  1. Select Tools> Component Configuration.
  1. In the Component Configuration Manager dialog, select the Genome Space checkbox.
  2. Click Apply.
  3. Click Close.

Using GenomeSpace in geWorkbench

When you click Workspace in the upper left corner of the screen, the GenomeSpace pane will appear to the right.

Log in by clicking the Login button next to the GenomeSpace Directories header, and now the GenomeSpace pane will display your directories.

You can work with your files within GenomeSpace:

Moving Files From GenomeSpace to geWorkbench

To move one of your GenomeSpace files into geWorkbench:

  1. If you do not already have a project in geWorkbench, right-click on Workspace and select New Project in the popup menu.

  1. Select a project.
  2. Right-click the file you want to use in geWorkbench and select Download in the popup menu.

Note that if you download a file that is not in a geWorkbench file format, GenomeSpace will convert it if there is a converter available.

Moving Files from geWorkbench to GenomeSpace

To move files from geWorkbench to GenomeSpace:

  1. Click the GenomeSpace tab.

  1. Right-click the file you want to move to GenomeSpace and select Upload to GenomeSpace from the popup menu.

  1. Select the GenomeSpace directory to which you want to upload the geWorkbench file.

  1. Click OK.

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