Bookmarks originally only saved location data and zoom; you needed to remember which files were open.
The updated Bookmarks feature now will record location information, zoom, but also which files were open at the time. This gives the user a huge advantage. As before, you can zoom in to a specific gene region and create a bookmark. When you open this bookmark again, it will zoom into that region. However, if the file is not open, or you are looking at a different species, IGB will now open the file that was bookmarked at the region of interest; you no longer have to reset IGB for the species, genome and file before using your bookmarks! IGB Bookmarks will now do this for you.
Another excellent use of this feature is to open a set of files with one click. Initially, you open each one of the multiple tracks of interest, at maximum zoom if there is not a specific region of interest. Then create a Bookmark. After that, one click of the bookmark opens the full set of files.
Bookmarks are still subject to the normal functionality of IGB. If you have Arabidopsis thaliana, 2009 genome open, but your bookmark is for the 2008 genome, when you open the bookmark, only the files listed in the Bookmark will be open. Tracks opened in the 2009 genome will go away. On the other hand, if you have a track opened in the 2009 genome for instance, and the bookmark is also from the 2009 genome, then the bookmarked files will open and maintain the originally opened track.
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Introduction
Use IGB bookmarks to:
- Jump to a bookmarked location and re-load data.
- Make notes on a genomic scene.
- Share analysis results with other users.
Bookmarks tab overview
The Bookmark tab allows you easy access to the bookmark list and provides tools for managing and sharing bookmarks.
IGB bookmarks tab with example bookmarks
Returning to a bookmarked region
To return to a bookmarked region,
- Double-click it
or
- Choose the bookmark from the Bookmarks menu
Bookmarks menu
Creating new bookmarks
To bookmark a location and data scene
- Choose Bookmarks > Add Bookmark
or
- Click Bookmarks tab
- Click add the New Bookmark icon
A window will appear with places to enter a name, notes, and bookmark type.
New bookmark window
Bookmark types
Position Only bookmarks record genome, current position and zoom level.
Position and Data bookmarks record genome, current position, zoom level, and data sets.
Managing bookmarks
You can sort your bookmarks into folders and associated comments with comments on folders.
To edit the name or comments associated with a bookmark or folder
- Click Bookmarks tab.
- Click to select a bookmark or folder.
- Edit name or comments in the Notes sub-tab.
To delete a bookmark or folder
- Click to select it
- Click the delete bookmark icon (red X) or press Delete
Exporting and Importing bookmarks
To save a copy of the bookmarks to a file
- Choose Bookmarks > Export Bookmarks...
To import another user's bookmarks
- Choose Bookmarks > Import Bookmarks...
Bookmarks are saved as a single file in an HTML-based format. Use caution if you choose to edit the file.
You can import multiple sets of bookmarks during the same IGB session. Imported bookmarks will be added to the end of the list of existing bookmarks.
Viewing bookmark properties (for advanced users)
To see when a bookmark was created and the region it refers to
- Click Bookmarks tab
- Click the bookmark to select it
- Click Location sub-tab
To see other properties of a bookmark
- Click Bookmarks tab
- Click the bookmark to select it
- Click Details sub-tab
or
- Click Bookmarks tab
- Right-click a bookmark
- Select Properties..
A new window will open that reports information about the bookmark and how IGB represents it internally.
To see how IGB combines these properties into an IGB bookmark, export your bookmarks and open the bookmarks file in a text editor to inspect bookmark syntax.
IGB bookmarks file
IGB saves your bookmarks at the end of each session in a file named bookmarks.html in a folder named .igb in your home folder.