GenoViz / News: Recent posts

Focus on a Feature for the month of October will look at the new features we are introducing with the upcoming IGB 8.0 release (look for it in December)!

We will have 2 sessions for this webinar, one at 9am EST (for early birds and users in Europe) and session 2 will be at 1pm EST (as per usual). Due to various scientific meetings, this month we will hold our webinar on TUESDAY, October 29, as opposed to the last Wednesday of the month. As always, your questions during the presentation are welcome and after the presentation, we open the floor to questions about any IGB topics you have.... read more

The next session of our new webinar series "Focus on a Feature" will be at 1pm (EST) on Wednesday, September 25. This session will focus on the Sequence Viewer. By highlighting how, as well as WHY, to use these features, we hope to expand the usefulness of IGB in your data analysis; your questions during the presentation are welcome! After each presentation, we open the floor to questions about the current topic, other topics, troubleshooting, feature requests or anything else you want to discuss.... read more

We will be running a webinar for new users of IGB on Wednesday, September 11 at 1pm; we will be going over the basics of opening and loading data, personalizing the environment and beginning analysis. This will be a great introduction for new members of the lab, new collaborators, or people who just want to see 'what else is out there'. The webinar will end with a question and answer session to make sure that everyone can immediately begin using IGB. Please note that there is a 25 person max for this webinar, first come-first serve. If you cannot participate, the recording will be available on the IGB Channel at YouTube. Additionally, look for more upcoming webinars, including additional "Intro to IGB" sessions.... read more

We have just begun our new webinar series "Focus on a Feature" which occurs at 1pm (EST) on the last Wednesday of each month. Each session will focus on a feature or group of features that are sometimes overlooked in IGB. By highlighting how, as well as WHY, to use these features, we hope to expand the usefulness of IGB in your data analysis; your questions during the presentation are welcome! After each presentation, we open the floor to questions about the current topic, other topics, troubleshooting, feature requests or anything else you want to discuss. ... read more

Hello IGB users and developers!

We have just launched IGB Channel on YouTube, showcasing tutorial videos as well as recordings of our new webinar series "Focus on a Feature". Stop by and add us to your subscriptions; we will send out an alert when a new video is added!

client features:
major memory improvements for graphs (SGR, Wiggle, etc.)
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 is now accessible)
assorted GUI enhancements and bugfixes

server features:
introduced beta version of GenoPub
a MySQL database stores the meta data and annotations on each dataset.
a web-based tool (developed using the open source Adobe Flex SDK) allows end-users to easily upload, annotate, organize, and secure their genomic datasets.
datasets are organized into a folder structure that supports multiple views (e.g. patient, disease, factor).
datasets can be restricted to particular user groups, enabling the controlled distribution of private along side public datasets.
See install instructions under das2_server/INSTALL.txt

IGB-6.0
client features:

• compiled with Java 6
• enhanced data source preferences page
• unification of "Pattern Search", "Name Search", and "Annotation Browser" tabs
• added "Restriction sites" tab by default
• 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... read more

IGB 6.0 Beta is available from http://igb.bioviz.org, based off of revision 4406.

IGB
* 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... read more

The IGB User Guide is now updated for IGB 5.5. It is available at http://genoviz.sourceforge.net/IGB_User_Guide.pdf.

We have made available a release of IGB 5.5.

IGB 5.5 is an incremental release, with UI improvements, enhanced memory management, and assorted bugfixes. (Please see the release notes for more details.)

IGB 5.5 runs in the 1.5 Java Runtime Environment or higher. (Versions after IGB 5.5 will only support Java 6.)

You can run the program with a default amount of RAM memory (1024m) simply by double-clicking on the jar file. To specify a larger amount of RAM, in order to allow loading larger data sets, you must start the program with a command such as:

java -Xmx2048m -jar <name_of_igb.jar>

We have made available an executable jar file of IGB 5.4.

IGB 5.4 has a unified QuickLoad, DAS/1, and DAS/2 interface, as well as other features. (Please see the release notes for more details.)

IGB 5.4 runs in the 1.5 Java Runtime Environment or higher.

You can run the program with a default amount of RAM memory simply by double-clicking on the jar file. To specify a larger amount of RAM, in order to allow loading larger data sets, you must start the program with a command such as:... read more

We have made available an executable jar file with a pre-release alpha version of IGB 5.0.

IGB 5.0 makes greater use of the DAS/2 protocol than earlier versions of IGB.

We recommend that you run it using Java Runtime Environment 1.5 or higher.

You can run the program with a default amount of RAM memory simply by double-clicking on the jar file. To specify a larger amount of RAM, in order to allow loading larger data sets, you must start the program with a command such as:... read more

We are pleased to announce that version 4.56 of IGB has been released. This is primarily a bug-fix update, but a few minor new features are added, such as the display of cytobands.

This version corresponds with the version described in the newly-updated User Guide.

Find these on http://genoviz.sourceforge.net

Note: Be sure to download the correct version. IGB version 3 is being downloaded more often than we would expect. IGB version 4.56 has many features and usability enhancements relative to that old version. I have updated the name of the old package to emphasize that it is out of date. You are still free to download it if it is of interest to you.

The IGB User Guide has been updated to include the most recent versions of IGB, up to February 2007.

You may download it in PDF form from the page http://genoviz.sourceforge.net/

Look for the link to "Manual (PDF)"

Integrated Genome Browser version 4.52 has been released. Release notes can be found at
http://genoviz.sourceforge.net/release_notes/igb_release.html

Integrated Genome Browser version 4.50 has been released. Release notes can be found at
http://genoviz.sourceforge.net/release_notes/igb_release.html

Integrated Genome Browser version 4.48 has been released. Release notes can be found at http://genoviz.sourceforge.net/release_notes/igb_release.html