December 15, 2014: IGB 8.2 released

The IGB development team is pleased to announce the immediate availability of the new IGB 8.2 major release. This release contains resolutions to over 200 issues, including many bug fixes and new features.

Major New Features:

Usability Improvement Highlights:

Power User Highlights:

Engineering Notes:


December 8, 2014: IGB 8.1.13 released

In preparation for our upcoming IGB 8.2 release, we have released a minor release with some minor bug fixes to our update notification system. With this notification system we will be able to notify users when we release IGB 8.2. This is important, because major releases cannot be pushed out silently, and require users to download a fresh copy of our software.


December 1, 2014: Updated JNLP Generator Service Released

In preparation for our upcoming IGB 8.2 release, we have released an updated and simplified jnlp generator web service. For more information, see: JNLP Generator Service


November 25, 2014: IGB 8.1.12 Released

We have released a minor patch to ensure our blast functionality is not impacted by an upcoming NCBI blast URL change, For more information, see:


September 10, 2014: IGB 8.1.11 Released

The IGB team is pleased to announce a new release of IGB. This new version fixes an error in SVG image export. Thank you to everyone who reported it. This new release also fixes BLAST search on gene models. Last but not least, we've modified our backup QuickLoad server code. Now, if the main IGBQuickLoad.org site is unavailable, IGB will automatically switch over to our mirror site. For more information on these changes and why we needed them, see:


Sept 2, 2014: Welcome aboard Nowlan Freese

Today we welcome Nowlan Freese, Ph.D., who joins the IGB team as a postdoctoral trainee. Nowlan will help us reach out to new users and also help existing users get greater value from IGB. Nowlan studied developmental biology as a graduate student at Clemson University and most recently did postdoctoral work at the Max Planck Institute. During his postdoc, Nowlan plans to build expertise in bioinformatics data analysis, using IGB and other tools.

July 30, 2014: IGB 8.1.10 Released

Today we released IGB 8.1.10, a minor release which includes a patch for the following bug


July 30, 2014: Notice: Windows 7/8 Java Webstart Bug introduced with Java 7 update 65 and Java 8 update 11

We have been able to confirm the latest releases of Java 7 and Java 8 have introduced a windows specific Java Web Start bug which is unfortunately currently impacting our users. This new bug impacts all past web start releases of IGB. We have submitted a bug report to Oracle, but will be releasing a workaround later today to resolve this issue for our users.

For more details on the bug see our Jira Issue (IGBF-136)


July 21, 2014: IGB 8.1.9 Released

Today we released IGB 8.1.9, a minor release which includes a patch for the following


July 08, 2014: IGB 8.1.8 Released

Today we released IGB 8.1.8, a minor release which includes a patch for the following bug


June 16, 2014: IGB 8.1.7 Released

Today we released IGB 8.1.7, a minor release which includes a patch for the following bug


June 10, 2014: IGB 8.1.5 Released

Today we released IGB 8.1.5, a minor release which addresses many small bugs and improves stability. The list below highlights some of the improvements.


May 30, 2014: IGB 8.1.4 Released

Today we released IGB 8.1.4, a minor release which a bug impacting the proper loading of BAM files from https locations


May 29, 2014: IGB 8.1.3 Released

Today we released IGB 8.1.3, a minor release which resolves several bugs and enhances the look and feel of several widgets for MAC OSX users.


April 16, 2014: IGB 8.1.2 Released

Today we released IGB 8.1.2, a minor release which resolves a critical bug


April 15, 2014: IGB 8.1 Released

Today we released IGB 8.1, a major release which includes enhanced integration with Galaxy.


March 19, 2014: IGB 8.0.4 Released

Today we released IGB 8.0.4, a minor release which retracts some functionality which was not meant to be included in the 8.0.3 release.


March 18, 2014: IGB 8.0.3 Released

Today we released IGB 8.0.3, a minor release which includes a few bug fixes as well as added support for custom jnlp launch files. We have also added a new JNLP Generation Service to bioviz.org to help facilitate the generation of custom jnlp launch files.


March 7, 2014: Dec 2013 human genome release (hg38) now supported in IGB

Today we add the latest human genome assembly (hg38) as H_sapiens_Dec_2013 to the IGB QuickLoad data repository. Now, when you visit the latest human genome by clicking the Mona Lisa image on the IGB start screen, the Dec. 2013 human genome assembly and RefGene annotations will automatically load. You can still view older versions by selecting them in the Current Genome tab. If you have questions, please feel free to get in touch! Send us a tweet or post a message on the IGB Discussion forum at SourceForge.


March 3, 2014: IGB moved to git repository hosted at BitBucket.org

Today, after many years of using svn, we migrated the IGB source code to a new git repository hosted on BitBucket. Using a distributed version control system git will make it easier for developers to contribute new ideas and new features to the project. Thank you David for managing the transition.


March 3, 2014: IGB 8.0.2 released

Today we released IGB 8.0.2, a minor release that corrects issues affecting heatmap graph style display, search, and bookmark exporting.


Feb. 24, 2014: IGB team welcomes new lead developer David Norris

UNC Charlotte Computer Science graduate David Norris re-joined the team today, taking over from Hiral Vora as lead developer on the IGB project. In his previous position, David worked at Red Hat on multiple projects and gained valuable experience in many aspects of open source software development. In his new position, he looks forward to using his knowledge and skill to improve IGB functionality for users. Welcome to the team!


Feb. 8, 2014: SR gene annotations updated for Arabidopsis TAIR10 genome

SR genes encode RNA-binding proteins that regulated and help to catalyze splicing. We've updated the gene symbols and descriptions for Arabidopsis SR genes so that IGB now follows the nomenclature recommendations from Barta et al (2010) Plant Cell. Code used to modify the annotation files is freely available from this repository at BitBucket.org.


Feb. 6, 2014: Older human genomes supported in IGBQuickload.org

In response to user requests, we've added two archival human genome assemblies (hg17 and hg18) to the IGBQuickload site. This will enable you to view gene model (refGene) annotations with HUGO gene symbols for these older releases similar to the latest release.


Jan. 3, 2014: Farewell Hiral

Today was Hiral's last day on the IGB team. After four years of great work, he is leaving for a new position at Deutsches Bank in the Research Triangle Park area. Thank you for your many outstanding efforts helping scientists get the most value from their data. Good luck in your new position!


Dec. 18, 2013: DAS2 retired

Today we retired the DAS2 servers hosted on IGBQuickload.org and BioViz.org. We also retired the Affymetrix Arabidopsis tiling array data sets as well as Affymetrix microarray probe set visualizations for most genome versions. Note that IGB can still open Affymetrix "link.psl" files, and so if you need to visualize the probe sets, you can download the files from Affymetrix and open them in IGB.


Dec. 17, 2013: Farewall Alyssa!

Today we say a sad "goodbye" to IGB Outreach and Testing Coordinator Alyssa Gulledge, who leaves us for a new opportunities in Atlanta. Thank you Alyssa for your many efforts and we wish you the best of luck. We will miss you!


Dec. 6, 2013: IGB 8 released

This new version of IGB has many improvements, including:


Oct. 30 - Nov. 2, 2013: IGB at Genome Informatics, CSHL

Ann presented a poster and gave demos introducing IGB 8 to attendees at the Cold Spring Harbor Genome Informatics Meeting. To test-run IGB 8, download and run IGB 8 preview.


Oct. 29, 2013: Focus on a Feature - Introducing IGB 8

This month hosted two sessions of IGB Focus on a Feature to introduce new features of IGB 8, scheduled for release in December. To test-run IGB 8, download and run IGB 8 preview.

In this live tutorial, we showed how to:

Also see the Announcement on the BioStars message board.


Sept. 25, 2013: Focus on a Feature - Working with Sequence Data


Alyssa Gulledge and Ann Loraine led an hour-long on-line Focus on a Feature webinar that introduced participants to some neat tricks you can do with the IGB Advanced Search tab, such as searching for transcription factor binding sites and mapping and visualizing PCR primer sequences. Ann started the webinar with a quick review of moving and zooming in IGB, and then Alyssa showed off the sequence manipulation and analysis features. Due to technical problems, we were only able to record Alyssa's part of the presentation. We'll post a video on the IGB YouTube channel as soon as we finish editing it. For a description of the webinar, see our announcement on the Biostars Web site.


Sept. 9, 2013: IGB 7.0.4 released


Today a new bug fix release debuted on the Bioviz Web site. No new features were introduced, only corrections to existing features and optimizations to improve IGB performance and stability.


Aug. 28, 2013: First Focus on a Feature - Graphs


To help IGB users get more out IGB, we've started a new monthly Focus on a Feature webinar to be held at 1:30 pm Eastern time on the last Wednesday of every month. The first Focus on a Feature event covered genome graphs and graph manipulations.


July 22, 2013: IGB 7.0.3 released


A new bug fix release was released today. As always, this release contains no new features, just fixes for bugs reported by users or the IGB testing team.


May 17, 2013: IGB Workshop at WiNGS


The IGB team led a hands-on workshop demonstrating how to use IGB at the Workshop in Next-Generation Sequencing and Metabolomics (WiNGS) held at the UNC Charlotte Center City campus on May 17. This two-hour workshop described using IGB to explore RNA-Seq data set from pollen, based on our article titled RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. A step-by-step Web-based tutorial from the workshop is available.


April 30, 2013: IGB 7.0.2 released


Today we released a new "bug fix" release of IGB. This releases introduces no new features, just fixes for bugs reported by users or the IGB testing team.


April, 2013: New IGB QuickLoad site for pollen


A new IGB QuickLoad site for pollen-related data sets is now available at igbquickload.org/pollen. The inaugural data set on the site is a 75-base, single-end RNA-Seq dataset from Arabidopsis pollen and seedlings. An in-depth analysis of these data appears in RNA-Seq of Arabidopsis pollen uncovers novel transcription and alternative splicing, published on-line in the journal Plant Physiology.


Feb. 11, 2013: IGB 7.0.1 released


A new minor release was released. This releases introduces no new features, just fixes for bugs reported by users or the IGB testing team. For the release announcement, visit this post on the GenoViz developers' list.


January 28, 2013: IGB 7.0 released


A new major release of IGB is available for download. Some of the new features in IGB 7.0 include:

For more information, visit New in IGB 7.0.


July 5, 2012: Fragaria vesca available in IGB QuickLoad


Fragaria vesca, also known as the woodland strawberry, is now supported at IGBQuickLoad.org as genome version F_vesca_Sep_2011. Currently, genomic sequence and gene predictions are available. We were able to add the data thanks to advice from Stephen Ficklin of the Main Lab at Washington State University. Note that the Main lab develops genome database resources for the rosaceae, also known as the rosids, including peach, apple, cherry as well as strawberry. For more information, visit GDR - Genome Database for Rosaceae.


June 5, 2012: IGB 6.7.2 released


A new minor release of IGB is available. This new release fixes a couple of reported bugs and adds new features, including:


June 5, 2012: Nematostella vectensis genome available in IGB QuickLoad


The IGB QuickLoad site now supports the Nematostella vectensis genome and annotations. We collected sequence data and annotations from Metazome, a database similar to Phytozome that provides access to a variety of animal genomes. Data provided include sequence along with gene model annotations, with linkouts to Google and Metazome.


May 17-18, 2012: IGB workshop at WiNGS


The IGB team at UNC Charlotte presented at the UNC Charlotte Bioinformatics and Genomics Department Workshop in Next-Generation Sequencing (WiNGS). On Thursday, Ann gave a talk describing IGB features and demonstrated using IGB to examine splice variants with RNA-Seq data. On Friday, she presented a two-hour interactive workshop on using IGB to view RNA-Seq data from Arabidopsis. Alyssa Gulledge helped organize the WiNGS workshop; she arranged practise talks for speakers, trained students, and helped keep things running smoothly. IGB slides and workshop materials are available for download:

If you would like to use the tutorials or slides in teaching, please let us know. We would be happy to share the originals with you so that you can customize the tutorials for your students.


April 13, 2012: Sorghum RNASeq data set added to IGBQuickload


We added a new RNAseq data set to the main IGBQuickLoad.org/quickload data site. The data are from an article titled Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid published in Oct., 2011.

These data include three replicates per sample type of sorghum root and shoot samples undergoing simulated drought stress and ABA treatments and their corresponding controls. This data set offers a unique look at the stress-regulated transcriptome of this highly drought-tolerant and hardy plant.

To deploy the data set, we downloaded the raw data files as .sra files, converted them to FASTQ format, and then aligned them onto the January 2009 release of the Sorghum bicolor genome using TopHat 1.3.3. We subdivided the alignments files into read alignments that mapped once (SM) or more than once (MM) onto the genome. We also generated tabix-indexed coverage (.bedgraph) and TopHat junction (.bed.gz) files for each sample.

To access the data in IGB, load the Sorghum bicolor genome Jan 2009. Open the folder named RNASeq. Data sets appear in subfolders SM (single- mapping), MM (multi-mapping), ALL (both multi- and single-mapping), and Juncs, junctions predicted by TopHat from spliced alignments.


Feb 9, 2012: IGB 6.7 released


Today we released a new version of IGB, which contains many new features and improvements. Just of few of these include:


Feb 6, 2012: New tutorials on working with RNA-Seq data available


Many users have asked us how to create files for visualization in IGB. This can be a daunting task, particularly when working with results from high-throughput sequenicng experiments.

To help users and the bioinformatics personnel who support their research, we have published two new tutorials describing how to use bioinformatics tools such as tophat, samtools, Jim Kent's faToTwoBit, and tabix to process and share next-generation sequencing data sets with lab members and collaborators using IGB and the simple IGB QuickLoad system.

To view the tutorials, visit the IGB Developer's Guide section titled Sharing data sets .

In the next few weeks we hope to add more tutorials that will help users make better use of their data and also get more familiar with the rich set of features IGB offers for visualization and analysis of genomic data sets.

If you have questions or suggestions, please let us know. Email aloraine - at - uncc.edu with your comments and requests. We will do our best to respond quickly and thoroughly to all enquiries.


Feb 3, 2012: NetAffx data back on line, hosted at UNC Charlotte


The data formerly available via the NetAffx DAS2 data source, including probe set alignments for Affymetrix array products, RefSeq genes, and chromosome bandingb patterns ("cytobands"), are now available again from the new DAS2 data source hosted at IGBQuickLoad.org.

As a convenience to users, we have re-activated automatic loading of gene models (the RefSeq genes data sets) and cytological bands for certain genomes, including the human genome. If you experience any further problems with these data sets, please let us know - email aloraine --at-- uncc.edu.

Many thanks are due to Scott Wood (UNCC College of Computing and Informatics) who helped us a huge amount in setting up the new site. Thanks are also due to IGB developer Hiral Vora who updated the DAS2 servlet code to support the Affymetrix data. Last but not least, we are also grateful to Dr. Ron Shigeta of Affymetrix for sending us the Affymetrix data. Thank you Ron, Scott, and Hiral for your efforts on behalf of the IGB user community!


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 the week 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:


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:


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 IGBbUser's Guide.

New features available in IGB 6.5 include:


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:


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:

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:


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:


September 29, 2009: IGB 6.0 released


Some new features are listed below:

IGB client features:

DAS/2 server features:


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 download TableView, visit TableView launch 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:


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.

IGB Poster

John Nicol and BiG Retreat attendee