Frequently Asked Questions

What is the Integrated Genome Browser?

The Integrated Genome Browser (IGB - pronounced "ig-bee") is an open source, freely-available desktop genome viewer implemented in the Java programming language. It differs from other desktop genome viewers in that it adapts advanced visualization techniques that information visualization researchers have shown can aid comprehension and exploration of large data sets.

For example, IGB implements include animated, one-dimensional semantic zooming; edge-matching on overlapping features; floating genome graphs; a zoom stripe graphic that helps maintain context; and more. Also, IGB is truly integrated; via a simple Web services approach, IGB makes it possible to view your data alongside publicly-available genome annotations and other lab's data sets. IGB also makes it easy for you to share your own data with the public or privately with collaborators.

IGB is the flagship product of the open source Genoviz project, which develops visualization software for bioinformatics and genomics. IGB is based on a library of visualization "widgets" called the Genoviz toolkit, the newest version of the Neomorphic Genome Software Developers Kit. Neomorphic was a bioinformatics software company started by graduate students from the Berkeley Drosophila Genome Project in the late 1990s.

In early 2000, Affymetrix purchased Neomorphic. In 2004, Affymetrix released the Genoviz toolkit and IGB as open source, free software.

For more information about visualization techniques for genomic data, see Loraine and Helt, 2002. To read a short paper describing IGB, see Nicol et al, 2009.

What happens when I download IGB using Java Web Start?

When you click the Start with Java Web Start button, IGB is downloaded from our site and run on your computer.

This is done through a mechanism called Java Web Start, which allows software applications to be downloaded and started by your Web browser. If your computer is relatively up-to-date, the software you would need to launch IGB using Java Web Start is probably already installed and ready to work.

What happens behind the scenes is that when you click the button, your browser downloads a JNLP file, short for Java Network Loading Protocol. JNLP files contain instructions telling your computer how to obtain and launch a particular software program - like IGB - from over the Web.

The Java Web Start mechanism built into your browser reads the JNLP file, determines where to get IGB, and then starts the download. Once the download finishes, IGB will launch.

Because it's inefficient to download the entire software program each time you want to use it, Java Web Start saves the software it downloads in a special directory (a cache) dedicated to this purpose. Each time you launch IGB, Java Web Start will check our site to see if there are any new versions available for the download. If there are, it downloads and launches the newer version. As a result, the software on your local computer stays up-to-date with the current release of IGB.

See also: Java Web Start page in Wikipedia.

What file formats are supported?

Dozens of file formats are supported. See the IGB User's Guide for more details.

How do I load annotations data?

The Integrated Genome Browser can load annotations data from three different kinds of data sources:

• local files on your file system,
• Distributed Annotation Servers (DAS/2)
• Distributed Annotation Servers (DAS/1)
• and IGB Quickload sites.

When you download and launch IGB from bioviz.org, IGB will request information about supported genomes from its default DAS and QuickLoad data sources as well as any custom data sources you've added.

When you choose a genome, it will next ask the servers to tell it more about the genome, such as the number and sizes of contigs or chromosomes, available data sets, and so on. IGB uses this information to populate the Data Sources listing in the Data Access tab.

When you choose one of the available data sets and click "Refresh Data," IGB will then start downloaing the data sets. However, some data sources may tell IGB to automatically load some basic data sets, such as the latest gene annotations for genome. This is done via the "load_hint" attribute in a servers "annots.xml" file. For more details, visit the http://www.igbquickload.org/quickload site. ers.

To view a genome and its annotations in IGB:

Click the Data Access tab in the lower part of the IGB screen; this tab is selected by default when IGB first launches.

Choose a species from the menu (e.g., Arabidopsis thaliana).

Choose a genome version from the available versions listed in the Genome Version drop-down menu box.

When you pick a species and genome version, a list of assembled sequences (e.g., chromosomes or contigs) will appear in the Current Sequence tab and a list of data sources will appear in the Data Sources table at the lower left of the display.

Click a Data Source folder to find out which data sets it provides. Some data sources may organize data sets into sub-folders.

Click a Data Set checkbox to start loading a data set. When you click a Data Set checkbox, it will disappear from the Data Sources table and re-appear in the Loaded Data Sets table in the middle of Data Access tab.

Choose a Load Mode for the data set. To load data for a small range, choose Region In View. The Refresh Data button will become enabled.

Use the sliders to zoom and scroll to the region you want, and then click Refresh Data to load data for that region. Each time you click Refresh Data, IGB will query its data source servers and get the data you've requested be loaded as Region In View under Load Mode.

To view a different chromosome or see the entire genome, click the corresponding row in the Current Sequence table.

How do I set up a QuickLoad site or directory?

Please see the IGB User's Giude or the IGB QuickLoad site for more details.

Who do I contact for help?

Please contact us to share comments and ideas. We welcome your suggestions!