IGB News

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 used 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 this 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.