Introduction to bookmarks in IGB
Bookmarks in IGB allow you to create a shortcut to a specific position and zoom level within a set of files. Clicking on the bookmark will tell IGB to zoom and scroll to the bookmarked position and zoom level in a file. Items that you bookmark will appear under the Bookmarks menu. When you create the bookmark, you will be able to provide any name 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 window 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 folds for each user to allow 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.
'Add file & position bookmark'
The original bookmark function ('Add position bookmark' ) only saves location data and zoom; you needed to remember which files were open and open them yourself. All bookmarks of this type remain valid and operational, but we have introduced an expanded bookmark function. The new 'Add file & position bookmark' function will not only remember the position and zoom level, but it will remember all the tracks in view at the time. This gives the user a huge advantage in that you no longer have to remember which files (either local or on the server) were loaded, nor which chromosome was being used. The user also no longer needs to open these files by hand. A simple click of the bookmark will open all of the associated files to the location and zoom level, as if 'load > region in view' were selected from the load menu. If the user is interested in a greater area than bookmarked, or on a different chromosome within those same files, using the zoom out/'current view > chromosome (X)' and refresh (one track at a time or all tracks) will load the rest of the regions of interest.
TIP: Another excellent use of this feature is to open a set of files with one click. If the user typically has a set of files that is used regularly, rather than open each one individually, you can set up a bookmark to open them all at once. Initially, you open each track; open at maximum zoom if there is not a specific region of interest and then create a Bookmark. After that, one click of the bookmark opens the full set of files.
In addition to remembering which files were opened, this expanded feature will remember many of the personal changes you made to the tracks such as color or height. Also, changes made to graphs such as threshholding will be saved.
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 be removed. On the other hand, if you have a track already opened in the 2009 genome for instance, and the bookmark is also from the 2009 genome, then any additional bookmarked files will open in conjunction with the originally opened track.
'Add position bookmark'
The old bookmark function is still sometimes useful; when sharing bookmarks involving local files where the recipient needs to load up those local files, the new Bookmark feature would not be able to find the file. By using the old 'Add position bookmark' the recipient can load the files themselves and then use the old-style bookmark to move to the location and the zoom level. However, once the location of the local file has been established on their computer, they can use the new 'Add file & position bookmark' to create a new bookmark that will record location and zoom, but also be able to open the local file(s).
Creating bookmarks
'Add position bookmark'. These record the currently shown genome, the location, and the current zoom level.
- To create, choose Bookmarks menu > Add position bookmark
'Add file & position bookmark'. These record the same things as position bookmarks, but also keep track of any graphs or files that you have loaded thus far. In addition to remembering the data files that you have loaded, position-and-graphs bookmarks can also remember many of your customizations for graph appearance, such as color, graph bound adjustments, thresholding, and labeling.
- To create, choose Bookmarks menu > Add position & graphs bookmark.
Using bookmarks
To load a view that you have bookmarked.
Choose Bookmarks menu > [name of your bookmark].
Viewing and editing bookmarks
You can view details about your bookmarks, such as their position, which genome they refer to, or customizations for position-and-graphs bookmarks. You can also modify some details, such as the name of a bookmark or customizations of a position-and-graphs bookmark.
To view or change bookmark details:
- Click Bookmarks menu > Manage Bookmarks.
- Select a bookmark.
- Right click the selected bookmark or click the Bookmarks menu in the Bookmark Manager window and then select the Properties button.
- The information will appear in tabular format in a new window.
- (Optional) Modify the bookmark details.
- Click Apply Changes or Cancel. Changes will not take effect unless you chose Apply Changes.
Exporting bookmarks
To save a copy of the bookmarks to a file:
- Click Bookmarks menu > Manage Bookmarks.
- In the bookmark manager window, choose Bookmarks menu > Export Bookmarks
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.
Importing bookmarks
You can import and use bookmarks, for example bookmarks that other people give you:
- Click Bookmarks menu > Manage Bookmarks.
- In the bookmark manager window, choose Bookmarks menu > Import Bookmarks > choose the file containing the bookmark of interest.
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.