Introduction

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In IGB 6.7 Bookmarks received a major redesign and had many new features added. Bookmarks in IGB allow you to create a shortcut to a specific genomic location and zoom level within a collection of data sets. Bookmarks are listed in the Bookmarks menu and in the Bookmarks tab.  When you create the bookmark, you will be able to provide any name and commentary, detailing elements in the bookmark. You can organize your bookmarks into folders, which can also have comments. There are tool tips for bookmarks, showing the chromosome number and coordinate range to further assist you in your data analysis. We have also included Bookmark history, with 'fast forward' and 'rewind' buttons allowing you to move back or forward through the bookmarks you have looked at/made during a particular session.

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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 ; it also provided 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. Finally, the Bookmark tab allows you to export or import IGB bookmarks; this allows these bookmark files to be shared between (distant) users. Note: We strongly recommend that you occasionally export and save your bookmarks to provide a back up file.

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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 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

In IGB 6.7, adding a bookmark either Bookmarks > Add Bookmark, or clicking the 'star plus' icon in the Bookmarks tab will open a new window. You can choose to have this window always offer you the default name (which is the Genome Version, followed by the chromosomal location) by leaving the Use Default Name box checked. You can change, add to or alter the name from this window. You can also add any commentary you like in this window, especially information about the experiments, what you analysis is, the lab who sent these bookmarks, etc. Anything you like can go in this box, and it will be remembered, but remain editable. Chose Position Only or Position and Data option (details below) and then click OK.
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Position and Data bookmarks

Position and Data is the default setting for IGB bookmarks. These bookmarks remember the genomic location and zoom level, plus all of the data sets loaded at the time the bookmark was made. This also includes background color selection, and changes to the name of the track. Using the bookmark will open all of the accessible data sets/ data sources to the marked genomic location at the original zoom level. Any data sets loaded from a password protected source will ask for the password. Any files not found (missing from original locations) will throw a warning, but all remaining files will load. After all the files have loaded, you can continue to load more regions and work as if you had loaded them 'by hand'. 

Much as using an internet browser bookmark will take you to a completely new page, using IGB bookmarks will clear away data from different species and/or genome versions and replace it with the data contained within the bookmark.  The one time that IGB does this differently is if the data sets that are open match the same species and genome version in the bookmark; in this case, IGB will just add data sets not already opened and zoom to the marked location. For instance, if you have open the 'TAIR10 ALL' data set from Arabidopsis thaliana, genome version June 2009 and your bookmark was made for the 'TAIR10 mRNA' data set from the matching species and genome version, when the TAIR10 mRNA bookmark is activated, it will add the TAIR9 mRNA data set, zoom in to the location and then display both the TAIR9 ALL and the TAIR9 mRNA tracks.

Position 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

To create a bookmark, choose Bookmarks > Add position & data Bookmark or Bookmarks > Add position bookmark. As you create bookmarks, both the Bookmark menu and the Bookmark tab will become populated with the list of bookmark names. To load a view from a bookmark, just click on the name of the bookmark in either list.

If you find that you need to organize your bookmarks, the Bookmark Manager or Bookmark tab has several options. First, simply click and drag the name of a bookmark to move it around within the list. You can create folders and sub-folders to group your bookmarks; you can also create separators to help with organization. Both the folders and separators can be created using the helpful side buttons (blue box). You can also delete a bookmark by selecting it and clicking the trashcan icon (purple box).

You can view details about your bookmarks, such as their position, which genome they refer to, or customizations. Right click the selected bookmark or click within the bookmark manager window the Properties button (left side or bottom button in red). This will open the Properties window with all of the information. If you make changes, click Apply Changes or Cancel;  changes will not take effect unless you choose Apply Changes. You can also modify the name of a bookmark from either the Properties window, or the helpful Name entry box (orange box).

Finally, as you can see (green arrow) we are currently looking at the second bookmark. We can use the history arrows (green box) to move forward or back through the bookmarks we have used in this session.

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, choose

• Choose Bookmarks > Export

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• 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. This file can be saved for back-up purposes and/or shared with othersunmigrated-wiki-markup

You can import bookmarks (red box), for example bookmarks that other people give you; choose *Bookmarks > Import Bookmarks > \[file name\].*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.