Introduction
Bookmarks in IGB allow you to create a shortcut to a genomic location and zoom level.
IGB bookmarks allow you to:
- Jump to a bookmarked location and re-load data
- View, add, or edit notes associated with the bookmark
- Organize and sort bookmarks into folders
- Use history buttons to revisit previously viewed bookmarks
- Import bookmarks from another IGB user
- Export bookmarks and share them with other IGB users
The Bookmark tab
The Bookmark tab allows you easy access to the bookmark list; it also provides all of the tools needed to manage and share the bookmarks. For more details about the 'anatomy' of this tab, see Bookmark tab.
The Bookmark tab permits folder, separator and bookmark creation and deletion (the Bookmark dropdown menu only allows adding of a bookmark) improving organization of bookmarks. It contains an editor so that names and commentary about the bookmarks and folder can be changed as each area is analyzed, or to track what lab shared these bookmarks.
The Bookmark tab allows you to export or import IGB bookmarks; this allows these bookmark files to be shared between users. Use this feature to backup your bookmarks or share them between computers.
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.
Note: If you need to reset preferences to default, or if you need to clear the IGB 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.
Adding bookmarks
Create a new a bookmark using the Bookmarks > Add Bookmark menu or clicking the 'page with blue bookmark' icon in the Bookmarks tab. This will open a new window. Enter a name for the bookmark or use the default name IGB provides, which is the Genome Version, followed by the chromosomal location. You can change, add to or alter the name from this window.
You can also associate a free text comment with the bookmark in the Comment box. Choose Position Only or Position and Data option (details below) and click OK.
Position and Data bookmarks
Position and Data is the default setting for new IGB bookmarks. These bookmarks remember the genomic location and zoom level along with the data sets loaded at the time the bookmark was made. Using the bookmark will open all of the accessible data sets/ data sources to the marked genomic location at the original zoom level. If the original data sources or files are no longer available, IGB will let you know.
Position Only bookmarks
Position Only bookmarks only contain the location data and zoom level; you need to open any associated data sets or file 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 or commentary.
Managing bookmarks
You can sort your bookmarks into folders and also associated with comments on folders.
To delete a bookmark or folder
- select it
- click the delete bookmark icon or type the Delete key on your keyboard
For advanced users:
You can view and edit bookmark properties, such as position, genome version, etc. To view or edit bookmark properties, right-click it and choose the Properties option.
Exporting and Importing bookmarks
To save a copy of the bookmarks to a file, choose Bookmarks > Export Bookmarks ('arrow up from the box' icon). 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 multiple sets of bookmarks during the same IGB session. Imported bookmarks will be added to the end of the list of existing bookmarks. Imported bookmarks will persist between sessions of IGB. You can modify the new folder for imported bookmarks, as well as add commentary to any of the imported bookmarks.