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 have IGB refocus to the marked 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. You can edit your bookmark list, as well as exporting and importing bookmark lists, with the Bookmark Manager window. 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 (the 'Add location bookmark' function) originally only saved 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. These bookmark files can be shared between (distant) users.
Add position & graphs 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 these bookmarks this type remain valid and operational, but we have introduced a new an expanded bookmark function. The new 'Add location and file position & graphs 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 presentbeing 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.
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 position and file bookmark' to create a new bookmark that will record location and zoom, but also be able to open the local file(s).
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