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To make IGB easier to use, we re-configured the user interface for several IGB tabs and panels including the
- Bookmarks tab
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- the Export File window
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- the Web Links Tools interface
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We also re-designed the IGB start screen. Now, when you start IGB for the first time, you'll see a new start screen that provides quick and easy access to a variety of model organisms, helping new users jump right in.
Credit for this new interface go to Dr. Jeremy Villalobos and Graduate Research Assistant David Norris.
Better Bookmarks tab - and support for comments
The Bookmarks tab now support comments for each bookmark and for supports adding comments to bookmarks and bookmark folders.
When you create a new bookmark, IGB will give you the option to add a free text comment. (As before, you can name bookmarks whatever you like or just use the IGB-supplied default.)
The Add Bookmark function offers the option of making one of two types of bookmarks:
- a Position Only bookmark which records genomic location
- or a Position and Data bookmark, which also records data sets currently being displayed
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Returning to a Position Only bookmark returns you to the bookmarked genomic position but won't load data.
Returning to a Position and Data bookmark returns you to the bookmarked genomic position and also re-loads data sets that were in the original scene (provided they are available).
Right clicking on the Position and Data a bookmark will open a new window displaying bookmark attributes, such as loaded data sets.
Thank you to Graduate Research Assistants Zhong Ren and David Norris for programming and also to Dr. Alyssa Gulledge for design and usability evaluation.
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We are also added a new feature that allows you to set image resolution/DPI. IGB now makes it easier to create high-quality images of 300 dpi or better (the minimum required for images destined for publication in printed journals).
Note to current users: Unfortunately, we had to remove export to PDF and other vector graphics formats. There were a number of show-stopping bugs in the external libraries we were using to support export in those formats. We are looking for new libraries that will be able to support those formats and hope to aim this functionality in the next release.
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A number of IGB ffeatures that require access to sequence data, such as Restriction Site mapping, the Sequence Viewer for gene models and Search Residues functions. Previously, IGB would ask you before loading sequence data. Starting with IGB 6.7, IGB will automatically load sequence data from available IGB QuickLoad or DAS sites, speeding the process of retrieving information you need for analysis and visualization. However, you can still Load Sequence in View or Load All Sequence information from the Data Access panel.
Tip: You can control which server IGB will use for accessing sequence data by changing the ordering of Data Sources in the Data Sources Preferences tab. Data providers differ on whether it is better to deliver masked versus unmasked genomic sequence to users, and so we decided to give users the ability to control which data source provides the reference genome sequence. Thanks are due to developer Lance Frohman (Genentech) who added this feature.
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