Bookmarks in IGB allow you to create a shortcut to a specific genomic location and zoom level within a collection of data sets. Bookmarks will be listed in the Bookmarks menu. When you create the bookmark, you will be able to provide any name or descriptor you wish to help you remember what the bookmark is for.
Any bookmarks that you create during a session will be saved when you exit, and will be available the next time you launch IGB. Bookmarks are saved in their own sub-directory, separate from the preferences and the cache. If you need to reset preferences to default, or if you need to clear the cache, your bookmarks will NOT be affected. However, if the entire IGB directory is deleted, or if the bookmark sub-directory is deleted, then all the bookmarks will be lost.
The Bookmark Manager will allow you to work with your saved bookmarks. It will allow you to edit your bookmark names, or edit the bookmark list. You can set up separate folders for each user, allowing for individual bookmarks; the Bookmark Manager will allow you to also switch between these folders. Finally, the Bookmark Manager will allow you to export or import IGB bookmarks; this allows these bookmark files to be shared between (distant) users. We strongly recommend that you occasionally export and save your bookmarks to provide a back up file. This will allow recovery of your bookmarks in case of catastrophic failure of the program.
As of IGB version 6.4 and higher, the expanded Add data & position bookmark function will remember the genomic location, zoom level, all the tracks in view at the time and any changes made to the track(s). This includes color selection, name of the track and/or changes made to graphs such as threshholding. Using the bookmark will open all of the data sets/ data sources to the marked genomic location at the original zoom level (as if Chose Load Mode > Region in View were selected) with color and name adjustments. If you are interested in a greater area than bookmarked, zoom out or chose a new region from Current Sequence and then refresh the relevant tracks.
Much as using an internet browser bookmark will take you to a completely new page, using IGB bookmarks will clear away data from different species and/or genome versions and replace it with the data contained within the bookmark. The one time that IGB does this differently is if the data sets that are open are from the same species and genome version; in this case, IGB will just add in any data sets needed and zoom to the marked location. e.g. Arabidopsis thaliana, genome version June 2009 is selected, and the TAIR9 ALL data set is open. Your bookmark was made for the TAIR9 mRNA data set, same species and same genome version. When the mRNA bookmark is activated, it will add the mRNA data set, zoom in to the location and then display both the ALL and the mRNA tracks.
The function Add position bookmark only bookmarks the location data and zoom level; you need to open the associated data sets or sources to use these bookmarks. Using this type of bookmark will zoom in to a genomic location and zoom level within the currently opened data. You may wish to indicate that this is a position only bookmark in the name that you create for this bookmark.
To create, choose:
or
To load a view that you have bookmarked.
Choose *Bookmarks > \[name of your bookmark\]* |
You can view details about your bookmarks, such as their position, which genome they refer to, or customizations. You can also modify some details, such as the name of a bookmark.
To view or change bookmark details:
To save a copy of the bookmarks to a file:
Bookmarks are saved in a single file in the Netscape bookmarks file format. This format resembles XML and HTML, but is not identical to either of those, so use caution if you choose to edit the file.
You can import and use bookmarks, for example bookmarks that other people give you:
In the bookmark manager window, choose *Bookmarks > Import Bookmarks > \[choose the bookmark file\].* |
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. All imported bookmarks will be persistent between sessions of IGB. You can create a new folder for imported bookmarks, if you do not wish them to mix with your current bookmarks.