Introduction

Bookmarks in Use IGB allow you to create a shortcut bookmarks to:

• Jump to a

...

• bookmarked location and

...

• re-load data.

When you create a new bookmark, you can add notes describing what you see. 

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 forward and back arrows allowing you to move back or forward through the bookmarks you have viewed or created during a session.

• 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.

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.

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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

Create a new a bookmark using the Bookmarks > Add Bookmark menu or clicking the 'star plus' 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. Anything you like can go in this box. Chose Position Only or Position and Data option (details below) and click OK.

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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.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 also 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 Click the delete bookmark icon or type the Delete key on your keyboard

For advanced users:

...

• (red X) or press Delete

Exporting and Importing bookmarks

To save a copy of the bookmarks to a file, choose

• Choose Bookmarks > 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.

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

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.