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There are three main ways you can load data into IGB:
An IGB Quickload site is simply a set of directories that contain "bulk" data files in IGB-readable formats, plus some additional files describing each available genome, the data files available for each genome, and so on. IGB can access Quickload sites saved on your local computer's hard drive or via the Web. If you want to see an example, click here to view the PlantQuickload site that PlantIGB uses.
The PlantQuickload site contains some mid-sized files with "bulk" data sets divided up by type. For example, the PlantQuickload site has Arabidopsis protein-coding genes (version 6 annotations) from TAIR that are formatted for loading into IGB.
You can load large data files from PlantQuickload over the network using the PlantQuickload data source option under the "Data Access" tab in IGB.
To load data this way, launch PlantIGB. After the main IGB window appears, click the Data Access tab. Then, choose a data source, genome, and chromosome as shown below. IGB's Data Source tab should then show some checkboxes with different bulk data sets you can load into IGB. To load a data set, just click its checkbox. After you've loaded a data set, the checkbox will looked grayed-out to prevent you from loading it again and also to let you know what data types are currently on view in IGB.
To load sequence for the currently displayed chromosome, click the "Load All Sequence" button. (Note: The "Load Sequence in View" button currently does not work -- we hope to correct this soon!)
Some of the data sources currently available to load into IGB include:
We are sorry to report that as of May 6, 2007, DAS service is temporarily unavailable due to a problem with the PlantGDB site, which supplies the data. We have notified PlantGDB of the problem and look forward to getting it back on line soon!
To open a file, just use the File->Open menu.
Tip: If files are compressed using gzip, IGB can still open and display the data without your having to uncompress the files first.
IGB understands a variety of file formats, but by far the best supported is the so-called "bed" format, which stands for browser extensible format that was developed by the University of Santa Cruz Genome Informatics group.
Other formats with varying levels of support include: