Introduction

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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.

'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. As of IGB version 6.4 and higher, the expanded '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 name of the track. 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'. (IGB version 6.4 and up) 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.

• Wiki Markup
  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.

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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
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Returning to a bookmarked region

To return to a bookmarked region,

• Double-click it

or

• Choose the bookmark from the Bookmarks menu

Bookmarks menu
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Creating new bookmarks

To bookmark a location and data scene

• Choose Bookmarks > Add Bookmark

or

• Click Bookmarks tab
• Click add the New Bookmark icon Image Added

A window will appear with places to enter a name, notes, and bookmark type.

New bookmark window
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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:

• Click Choose Bookmarks menu > Manage Export Bookmarks.In the bookmark manager window, choose Bookmarks menu > Export Bookmarks...

To import another user's bookmarks

• Choose Bookmarks > Import Bookmarks...

Bookmarks are saved in as 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 an HTML-based format. 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:

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the file

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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

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.