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 location data and zoom; you needed to remember which files were open. All of these bookmarks remain valid and operational, but we have introduced a new bookmark function. The new 'Add location and file 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 present. 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.

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).

Creating bookmarks

Before you add bookmarks, make sure you are not running multiple instances of IGB. 

There are two types of bookmarks in IGB:

• Position bookmarks. These  record the currently shown genome, the location, and the current zoom level. 
  • To create, choose Bookmarks menu > Add position bookmark
• Position-and-graphs bookmarks. These record the same things as position bookmarks, but also keep track of any graphs 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 changing bookmark details

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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Introduction

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:

• 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.

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 .  All imported bookmarks will be persistent between sessions of IGBand 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.