IGB News

January 31, 2012: Temporary service outage for IGBQuickload.org

We apologize for the inconvenience.

Starting around 1 pm EST today, the IGB QuickLoad resource will become temporary unavailable.

We are adding more memory to the server and installing some new software. We don't expect to be off-line for more than a couple of hours at the most.

You may have noticed that the NetAffx DAS2 data source is no longer responding. Unfortunately, there was an irrecoverable failure in the DAS2 data source hosted at Affymetrix. We are working on a solution and should have the data sets Affymetrix was hosting back on line; we are moving the data to a virtual server residing at UNC Charlotte.

In the meantime, we've deactivated the NetAffx DAS2 data source as one of the default IGB data sources. Hopefully by the end of today or by early tomorrow you will have full access to the data once again.

January, 2012: IGB 6.7 alpha available on BioViz Web site.

A preview (alpha) release version of IGB 6.7 is now available on the BioViz Web site. Just visit the Download Page to get a copy.

Note to programmers: The IGB 6.7 release version is now branched in the subversion repository on sourceforge.

New features coming soon in IGB 6.7 include:

• Better data loading: When you access a file, a "blank" track appears letting you know that IGB recognized your file.
• Better bookmarks: Now, when you make a bookmark, you can add a note describing it. You can also more easily edit, move, delete, and share your bookmarks.
• All-new start screen: We added shortcuts to the IGB start screen, making it easier than ever to find your genome of interest.
• Better support for image export: We improved the way that images are created, adding the ability to increase or decrease image quality. Now it's easy to create high-quality (300 dpi or better) images for publication.

October, 2011: IGB 6.6 released

IGB version 6.6 is released on the BioViz Web site. To read about new features and improvements in this new version of IGB, see New in IGB 6.6 in the IGB User's Guide.

New features in IGB 6.6 include:

• Improved Data Access Panel. You can now use the Data Access Panel to change track colors, hide or show tracks, or double-click in the Track Name column to re-name a track.
• New Options for Configuring Tracks. You can now use arrows or color to indicate strand for features and/or sequence read alignments. You can also increase or decrease the font track label font. Choose File->Preferences to configure tracks, or just right-click a track label and choose the Configure option.

June, 2011: IGB team at ICAR 2011

The IGB team is hosting a booth at the International Conference on Arabidopsis Research in Madison, WI. We'll be giving one-on-one demos and answering questions about using IGB in research.

Ann gave a talk on IGB - slides are available here. David Norris and the IGB team presented a poster.

April, 2011: IGB 6.5 released

IGB version 6.5 is now available for download from the BioViz Web site. For details, see: New in IGB 6.5 in the IGB User's Guide.

New features available in IGB 6.5 include:

• Sequence Viewer. View, translate and copy sequence in a new user-friendly interface.
• More ways to zoom and pan. Use the new grab tool to move the display up or down, left or right.
• Insertions and deletions. View insertions and deletions in alignment (BAM) files.
• Expanded support for plant genomes. The IGB QuickLoad site now hosts data for publicly available plant geomes including grape, soy, rice, Arabidopsis lyrata, and more.

January 15-19, 2011: IGB at the Plant Animal Genomes Conference

Ann is attending PAG XIX and giving a live demo of IGB at 10:30 am on Wednesday in the Computer Demo Room. Please read the abstract from the demo. We hope to see you there!

November 22, 2010: IGB 6.4 released

Thank you to everyone who tried IGB 6.4 Alpha and gave us your feedback. IGB 6.4 is now available and incorporates many of your suggestions.

October 22, 2010: IGB 6.4 Alpha released - Please try it out!

IGB 6.4 ALPHA is now available for preview on BioViz. Please visit the IGB 6.4 preview page to download a copy.

Thank you very much to everyone who responded to the IGB survey back in April 2010. You contributed many great ideas to improve IGB and we were able to implement many of them in IGB 6.4. Check it out and let us know what you think!

As always, please report any problems you encounter - just choose "Report a bug" or "Request a feature" from the IGB Help Menu. We now have a dedicated testing group for IGB, but we continue to rely on YOU for help making certain IGB performs well for your research.

New features available in IGB 6.4 include:

• Better Bookmarks. You can now bookmark data sets and current view settings. With new and improved IGB bookmarks, you can retrieve not just the region, but also the data together with color, display name, and other settings.
• Data Access tab You can now delete tracks. You can also refresh one track at a time without having to change the Load Mode settings in the Data Access Panel.
• Tracks and Tiers. When you mouse over a track label or feature in a track, you'll see a tooltip showing the same information as what appears in the Selection Info table. But if it's too much information, you can turn off the tooltips using the View menu.
• Searching. Now searching works for all feature properties, not just names. Note: This only works for data that you've already loaded.
• Loading data - for power users. If you're sharing a genome using an IGB QuickLoad data server, you can now use BNIB or 2BIT sequence file formats on your site and your users will be able to click the Load Sequence in View button to get just the sequence in view. (This happens via partial HTTP requests.) We also now support PSLX file format, an alignment format similar to PSL but which also includes query sequence.
• Scripting - for power users. We fixed some synchronization issues that were forcing some of you to tell IGB to wait before completing a script.

September 27, 2010: IGB 6.3.1 released

IGB 6.3.1 incorporates several bugfixes to IGB 6.3.

September 22, 2010: Alyssa Gulledge joins IGB team

The IGB team here at UNC Charlotte welcomes Alyssa Gulledge, Ph.D., our new testing, outreach, and documentation coordinator. Before joining us, Alyssa worked as a scientist and postdoctoral researcher at UNC Chapel Hill and UNC Charlotte.

July 21, 2010: IGB 6.3 released

Some new client features are listed below:

• BAM parser
  • (Be sure you've sorted and indexed your BAM files!)
  • Shows gapped alignments and properties.
  • When zoomed in, shows residues. If partial or full reference sequence is loaded, shows only differing residues.
• Local files and QuickLoad: allow partial (chromosome) feature loading for most formats.
• Local files and QuickLoad: allow region-based feature loading for BAM, BED, Wiggle, Sgr, Gr, Fasta, and others.
• Drag and Drop for files and (file or QuickLoad) URLs.
• "Load from URL" menu item. Allows region-based feature loading for BAM.
• Scripting options for IGB. See this Wiki page for more details.
• Deletion of tracks.
• Ensembl external browser (also loadable via DAS).
• Load View: combo box hints for species (common name) and genomes (synonyms).
• Whole genome view for all organisms.
• Sort chromosome list by contig/chromosome size
• Centralized server caching of common requests from slower servers (mostly UCSC and Ensembl).

As always, old versions of IGB are also available from our download page.

July 19, 2010: Slime mold Dictyostelium discoideum strain Ax4 genome data added

Using data and advice kindly provided by the dictyBase team, we created BED and sequence data files so that Dictyostelium researchers can view their data in IGB. The BioViz DAS2 data source now provides DAS2-style access to Dicty Ax4 sequence data, and the BioViz QuickLoad site now provides access to BED format files for dictyBase Dictyostelium discoideum strain Ax4 gene annotations. When you view the data in IGB, you can right-click on gene models and choose the "DictyBase" option to view the corresponding record in dictyBase.

For more information about the data, visit the Dicty May 2009 QuickLoad Web directory.

June 25, 2010: IGB 6.3 Beta released

April 8, 2010: IGB 6.2.1 released

Some new client features are listed below:

• DAS/1 support
• External UCSC browser tab
• Localization
• GUI and Preferences bugfixes and enhancements
• USeq support

March 26, 2010: IGB at the ASPB meeting

Ann gave an IGB demo at the Mid-Atlantic Section American Society of Plant Biologists Annual Spring Meeting, held at Bowie State University in Maryland. Slides from the talk are available on-line.

January 9-13, 2010: IGB at the Plant Animal Genomes Conference

Ann attended PAG XVIII, gave a live demo of IGB, and presented this poster.

January 6, 2010: IGB 6.1 released

Some new client features are listed below:

• major memory improvements for graphs (SGR, Wiggle, etc.)
• ability to parse large Wiggle files
• better handling for large files over network
• customizable coloring for residues
• "whole chromosome" mode for DAS/2; only activated when data is refreshed
• enhanced DAS/1 support (Ensembl can now be accessed)
• assorted GUI enhancements and bugfixes

September 29, 2009: IGB 6.0 released

Some new features are listed below:

IGB client features:

• compiled with Java 6
• enhanced data source preferences page
• unification of "Pattern Search", "Name Search", and "Annotation Browser" tabs
• auto-loading of features (if specified by DAS/2 server)
• data provider hyperlinks and icons
• feature hyperlinks and description tooltips
• QuickLoad annots.xml file (similar to DAS/2)
• GFF and BED parsing bugfixes
• warnings for chromosome conflicts
• assorted GUI enhancements and bugfixes

DAS/2 server features:

• file indexing: reduces memory requirements by up to 90%, often reducing startup time as well.
• improved ID searches: reduces network traffic, thus speeding up client-side search.
• warnings for chromosome conflicts
• additional annots.xml properties

September 11, 2009: IGB Wikipedia article published

August 25, 2009: Genoviz SDK article published in BMC Bioinformatics

Helt, G.A., Nicol, J.W., Erwin, E., Blossom, E., Blanchard, S.G., Chervitz, S.A., Harmon, C. & Loraine, A.E. The Genoviz Software Development Kit: A Java toolkit for building genomics visualization applications. BMC Bioinformatics 10, 266 (2009).doi:10.1186/1471-2105-10-266

August 4, 2009: IGB article published in Bioinformatics

Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. & Loraine, A.E. The Integrated Genome Browser: Free software for distribution and exploration of genome-scale data sets. Bioinformatics (2009).doi:10.1093/bioinformatics/btp472

June 16, 2009: IGB version 5.5 released.

This release features improved memory management, allowing users to load even more data into the viewer, as well as further streamlining of the user interface. Other improvements include support for adding new Quickload or DAS servers via the Preferences Tab and better image export support (print to file) for many formats, including PDF, PNG, EPS, PS, and others. For more details, see the IGB Release Notes.

May, 2009: The IGB team welcomes four new students and bids farewall to Lokeshvar

The IGB team welcomes two new students from the UNC Charlotte Professional Science Masters Program who are doing their internships with us this summer. Archana Raja is working on documentation, testing the user interface, and collecting tiling array data sets for our DAS2 server. Nathaniel Watson is collecting data sets from sequenced plant genomes so that we can support other plant species in addition to Arabidopsis. We also welcome two new undergraduate summer interns: Kristen Sagliani, a chemistry/math double major from UNC Charlotte and Roshonda Barner, a math/economics double major from NC A & T. Kristen and Roshonda are helping develop an on-line programming course that demonstrates bioinformatics programming concepts using data set from the Bioviz DAS2 and Quickload servers. We also bid farewell to Lokeshvar, who starts a new internship at Wachovia this summer. Good luck with your new job and thank you for your great work on IGB.

March 26, 2009: IGB version 5.4 released

We are pleased to announce the release of version 5.4 of IGB, which features a much improved mechanism for loading data into the browser. Users can now access Affymetrix DAS2, Bioviz DAS2, and Bioviz Quickload data sources using the same easy-to-use interface. For details on how this works, see the FAQ item describing how to load data into IGB.

March 12, 2009: Welcome aboard, Lokeshvar

The IGB team welcomes Lokeshvar Iyanar, who starts his new position as test and automation engineer today. Lokeshvar is working toward his masters' degree in Computer Science from the University of North Carolina at Charlotte. Previously, he worked as a Performance Test Analyst at for Wachovia and as a Student Technical Specialist at the Mosaic Lab at UNCC.

March 9, 2009: TableView Support

We have added a new Java Launch page for James (Jim) Johnson's TableView application, originally hosted at the University of Minnesota's Center for Computational Genomics and Bioinformatics, which closed in 2008. Jim's software is very useful for visualizing interactive scatter plots, a feature many IGB users may find helpful when working with expression array data. To launch TableView, visit the software links page. Let us know if you have questions or comments!

Jan. 7, 2009: IGB supports Arabidopsis EST data.

We used Jim Kent's genomic alignment tool blat to align around 1.5 million Arabidopsis thaliana ESTs harvested from Genbank in December 2008 onto the TAIR8 Arabidopsis genome assembly. We then applied a simple quality-control filter, following the same specification the UCSC Genome Informatics team uses to generate their "all EST" data set, with one important difference: We divided the alignments into two separate data sets:

• single mappers: ESTs that aligned once to the genome
• multi-mappers: ESTs that aligned more than once to the genome

Dec. 10, 2008: IGB poster at UNC Charlotte Bioinformatics and Genomics Retreat

IGB developer John Nicol presented a poster describing his contributions to the IGB and Genoviz projects at the UNC Charlotte Bioinformatics and Genomics Retreat. Here John discusses his work with an attendee at the event.