New Features in IGB 6.7
Welcome to IGB 6.7! . We have made many changes and improvements to make IGB even easier to use.
Many changes, such as moving the Species and Genome Version to Current Sequences tab and the redesigned Bookmarks tab willl will be immediately obvious to IGB veterans, but there are many more new and exciting functions you should explore in IGB 6.7.
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Major thanks are due to IGB software developer Hiral Vora, who led the effort and kept us all on track for the current release. Thank you Hiral!
Panels and tabs redesigned
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
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- 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 Jeremy Villalobs (programming), David Norris (programming), and Ann Loraine (design and image editing)Dr. Jeremy Villalobos and Graduate Research Assistant David Norris.
Better Bookmarks
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tab - and support for comments
The Bookmarks tab now 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,
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- which also records data sets currently being displayed
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 the properties window with a listing of the files that were loaded, as well as time/date created and genome version that was in use. In combination with the redesigned panel, users will find Bookmarks to be more helpful for visualizing, analyzing and sharing data than evera new window displaying bookmark attributes.
Thank you to Graduate Research Assistants Zhong Ren and David Norris for programming and also to Dr. Alyssa Gulledge for design and usability evaluation.
New options for exporting image files
Along with a redesign to improve ease of use, the Export interface also features new options not previously available. Users can now specify image size , and file type , and image resolution (DPI) for export. If you are using IG to make figures for publication in print journals, you'll need the ability to create high-quality, high-resolution images necessary for publicationfor export. You can still specify which part of the IGB display you'd like to export, e.g, the main display image, the main image with the track labels, or the entire window with tabbed panels (such as Selection Info) showing. IGB can currently export images in PNG or JPEG formats.
We are also added a new feature that allows you to set image resolution/DPI. IGB now makes it even easier to create high-quality images of 300 dpi or better (the minimum required for images destined for publication in printed journals). You can still specify the type of image -- e.g, the main display image, the main image with the track labels, or the entire window with panels (such as Selection Information) showing. You can export images as .png or .jpeg files and use these images for publications, slides, or sharing data with colleagues.
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.
Thank you to Zhong Ren (CS Masters student) for programming the Export Image window.
Autoload for features that use sequence data
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IGB has many features A number of IGB ffeatures that require laoding 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. Starging Starting with IGB 6.7, IGB will automatically load sequence data from available IGB QuickLoad or DAS sites, speeding the process of retrieving the 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.
New features for Main View:
We added several new features to the main view to improve the user experience. One new feature creates a track immediately after opening a file or accessing a data set under the Data Access panel, even before you load the data into the main view. This is where the data will appear once after clicking the Load Data button. Another feature to improve interaction with displayed data, is that the arrow cursor changes to a hand/pointer when your mouse passes over selectable features, indicating that you can interact with these items. 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.
Expanded residue Search function displays multiple sequences
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With IGB 6.7, we have introduced the ability to overlay multiple sequence Search results (up to 7 different searches).
The basic Search Residue function hasn't changed; as before, you type in the sequence you are searching for and IGB returns a list of 'hits' and marks on adds colored bars to the sequence bar indicating the exact location(s) using a color segment. With location of matches.
However, if you check the new Overlay option activated, subsequent residue searches will be added to the list and highlight highlighted in new colors , all at the same time. This is a powerful tool for many purposes! It can be used for showing multiple PCR primers in their accurate positions, aligned in the area of interest; it can show up to 7 enhancer, inhibitor or other elements in a promoter region, all in their accurate relationship to one another; the list goes on!without removing previous search results.
Use this new feature when you need to display multiple sequence features in the same view, such as forward and reverse primers for PCR primers, transcription factor binding sites, and so on.
Thanks are due to Dr. Alyssa Gulledge for designing and testing this new feature.
This image shows the 3 primers needed for determining splice variant choice for the AT1G07940 gene of Arabidopsis thaliana, all overlayed into shown in the same imageview.
Expanded file types and increased save options
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We are always expanding our ability to support new file types. With IGB 6.7, we can now support BedDetail files and tabix indexed GFF files. If there is a file type we don't support yet, let us know! IGB has allowed users to save annotation tracks (including tracks created through Track Operations) as .bed files. Now, IGB can now save graph tracks (including tracks generated with IGB tools in the Graph Adjuster panel!) as .bedgraph files.