IGB User's Guide
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Introduction

When you download and launch IGB for the first time, you will have a set of default data sources configured.  As of July 2010 (IGB version 6.3), these include:

  • NetAffx (Affymetrix) DAS2 service
  • NetAffx (Affymetrix) QuickLoad server
  • BioViz (Loraine lab) QuickLoad server
  • BioViz (Loraine lab) DAS2 service
  • Hughes Lab QuickLoad server (S. pombe data)
  • UC Santa Cruz Genome Browser original "classic" DAS service (note: this server does not have CDS data)
  • Ensembl original "classic" DAS service (includes many plant genomes not supported by UC Santa Cruz)

You also will have access to a few others, which are de-activated at first. However, you may activate them if you like.  You can also add more of course, including your own custom genomes.

Adding or Removing a New Data Source

Choose File  > Preferences > Data Sources or click the Configure button on the Data Access Panel to open the data sources configuration panel:

When you click the Configure button (or choose File > Preferences > Data Sources) you will see a window that looks like the image below.

Note how each data source has a Type, a URL, and an Enabled checkbox.

To turn a source off or on, click the Enabled checkbox.

When data sources are disabled, IGB will show them as grayed out. To remove a data source from the list, click on it to select it and then click the *Remove button.

To add a new data source, click the Add button. You will then see a window that looks a bit like this:

To add the data source,

  1. Enter a name for your new source:  The name can be whatever you like - this name will appear in the Data Sources section of the Data Access Panel. 
  2. Choose the type of the data source:  The current options are DAS2, original "classic" DAS, and QuickLoad.
  3. Enter the URL associated with the Data source:  If your data source is a QuickLoad site IGB will activate the button which will allows you to choose a local folder, since QuickLoad sites can either be on a remote computer (accessible via a URL Web address, such as http://www.bioviz.org/quickload) or a folder on your local computer. 
  4. Click Add Server or Cancel. If you click Add Server, IGB will immediately add your data source to the list of available data sources.

Troubleshooting:  If the data source has a problem - for example, if it is missing an important configuration file, IGB will print error messages to the Console that may help you diagnose the problem.  Choose the Help > Show Console to view the error messages. The next step is to remove and reenter the server (see Fixing invalid server address). If this doesn't help, contact the IGB team for assistance, or post a help request to the IGB Help Forum.   

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