IGB 4.02 to 4.12 release notes.

Highlights:

Version 4.12
- Bugfixes, such as making sure to read the das_servers.txt file from QuickLoad servers
Version 4.10:
- Added support for multiple QuickLoad servers
- IGB will start-up on the Genome and Sequence you were last looking at
- The known bugs from version 4.02 have been fixed
Version 4.02:
- User preferences are specified in a graphical interface
- The igb_prefs.xml file is being deprecated
- Added support for data-loading from DAS/2 servers
- Various bug fixes and enhancements

User preference changes

The igb_prefs.xml file is being deprecated.

In versions 3.x, users had to set preferences, such as annotation colors in a file called igb_prefs.xml. This file was difficult to edit and did not allow the changes to be immediately seen.

With version 4, the igb_prefs.xml file is almost obsolete. The majority of users should ignore this file. (Very advanced users may still find a few uses for it.) If you are still sometimes using older versions of IGB, you may choose to keep your igb_prefs.xml file in place. Version 4 will simply ignore most of the contents.

Setting annotation preferences

When you first load annotation data into IGB, all types of data will be displayed in the same default color and style. By default, only "RefSeq" data will display labels.

You can change some properties just as before, by right-clicking on the tier labels and choosing "Hide", "Collapse", "Expand", "Adjust Max Expand", or "Change Annotation Color". The main difference now is that these changes will be persistent. If you shut down the program and restart it, these settings will remain. (Except that hidden tiers will become visible again when you restart and reload that data.)

To access more advanced features, right-click on the tier labels and choose "Customize". Alternatively, you can access the same customization panel by choosing the "File->Preferences" menu.

From the tier preferences panel, you can

set foreground and background colors,
change the displayed tier names
combine (+) and (-) tiers into a single (+/-) tier,
collapse or expand tiers,
change the maximum tier heights,
choose to draw data without connecting lines (appropriate for "repeats" and "contigs"),
choose to display labels.

You may also change the default values of most of these properties. (A few of the default values are protected from changes.) For more details, use the "Help" menu on the preferences panel. Changes take effect as soon as you close this window.

Regardless of whether you set properties from the preferences panel or by right-clicking a tier, the properties will persist between sessions. Settings for temporarily-created tiers, such as from the union of two tiers, do not persist between sessions.

One other change to note: forward and reverse strands of the same annotation type now must have matching colors and styles. Changing one strand automatically changes the other as well. (We may later revise this to allow strands to be hidden independently.)

Remaining features of igb_prefs.xml

Advanced users may still choose to specify the location of a QuickLoad server in igb_prefs.xml, or to specify URL's that can be used by the "Get More Info" hyperlinks.

Here is an example of how to set the QuickLoad URL, and how to add a hyperlink.


<tagval tag="QuickLoadUrl" val="http://netaffxdas.affymetrix.com/quickload_data/"/>


<annotation_url annot_type_regex="EnsGene"
    url="http://www.ensembl.org/Homo_sapiens/textview?idx=All&q=$$" />

In version 4.02 the URL set this way in the "igb_prefs.xml" file will replace the standard NetAffx QuickLoad URL. (Due to a bug, any server set with the "Options" button in the QuickLoad panel will be ignored.)

In version 4.10 and higher, you are allowed to have multiple QuickLoad servers. You will always have access to the NetAffx QuickLoad server, and you may add an optional "Personal" server using the "Options" button in the QuickLoad panel. To maintain compatibility with earlier versions, if a QuickLoad URL is also set in the "igb_prefs.xml" file, it will become a third, "Auxiliary" QuickLoad server.

DAS/2 servers

Beginning with version 4.02, there is support for loading data from DAS/2 servers.

Earlier versions already had support for loading data from DAS servers. However, there is a new form of DAS server, DAS version 2.0, that is under development. Refer to http://biodas.org/ for more information on the DAS/2 specification.

Two experimental DAS/2 servers are available now. Feel free to test them, but be aware of their experimental nature. Until the DAS/2 specification becomes stable, you will generally need the most recent version of IGB to use these experimental servers.

DAS/1 servers

You may continue to access DAS/1 servers as before, using "File->Load DAS Features".

If no DAS/1 servers are listed when you try that, or if you wish to add additional servers, you may add servers with "File->Preferences" in the "DAS Servers" panel. These two servers are a good place to start: "http://genome.cse.ucsc.edu/cgi-bin/das/" and "http://netaffxdas.affymetrix.com/das/"

Bug Fixes

There are various smaller enhancements and bug fixes, including:

enhancements and fixes in the "Pivot View"
curations have been disabled, but will return in improved form in a future release
the Graph Adjuster tab has been simplified somewhat
problems with "right-clicking" graphs on Macintosh have been resolved

Known Bugs in Version 4.02

Unfortunately, a few bugs were introduced with release 4.02. These bugs were fixed in version 4.10.

QuickLoad server: The graphical interface for setting the location of the QuickLoad server does not work in version 4.02. If you need to use a server other than the default one, you will need to edit your "igb_prefs.xml" file.

For example on Linux:
<tagval tag="QuickLoadUrl" val="file:///home/steve/quickload/" />
or on Windows:
<tagval tag="QuickLoadUrl" val="file:///c:/Documents and Settings/name/quickload/" />

Tier Labels: If you change the tier label display name through the tier preferences panel, the name may not take effect until you re-start the program. Likewise, if you change from displaying forward and reverse strands separately to displaying them together, the label may not update to reflect this change, although the data will be drawn in one or two tiers as you requested.