...
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.
...
Data & position
...
bookmarks
As of IGB version 6.4 and higher, the expanded 'Add file data & position bookmark' function will not only remember the position and genomic location, zoom level, but it will remember all the tracks in view at the time and any changes made to the track(s). 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 includes color selection, name of the track and/or changes made to graphs such as threshholding. Using the bookmark will open all of the associated files data sets/ data sources to the marked genomic location and at the original zoom level , (as if 'load > region in view' were selected from the load menu. If the user is Chose Load Mode > Region in View were selected) with color and name adjustments. If you are interested in a greater area than bookmarked, zoom out 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.
...
chose a new region from Current Sequence and then refresh the relevant tracks.
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 are from the same species and genome version; in this case, IGB will just add in any data sets needed and zoom to the marked location. e.g. Arabidopsis thaliana, genome version June 2009 is selected, and the TAIR9 ALL data set is open. Your bookmark was made for the TAIR9 mRNA data set, same species and same genome version. When the mRNA bookmark is activated, it will add the mRNA data set, zoom in to the location and then display both the ALL and the mRNA tracks.
Position bookmarks
The function Add position bookmark only bookmarks the location data and zoom level; you need to open the associated data sets or sources 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 that you create for this bookmark.
Creating and using bookmarks
To create, choose:
- Bookmarks > Add position & data bookmark
or
- Bookmarks > Add position bookmark
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 within the Bookmarks menu in the Bookmark Manager window and then select the Properties buttonbookmark manager window Bookmarks > Properties.
- 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.
Exporting and Importing bookmarks
To save a copy of the bookmarks to a file:
- Click Bookmarks menu > Manage Bookmarks.
- In the bookmark manager window, choose Bookmarks menu > Export Bookmarks
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 and use bookmarks, for example bookmarks that other people give you:
- Click Bookmarks menu > Manage Bookmarks.
menuWiki Markup In the bookmark manager window, choose *Bookmarks
file containing the bookmark of interest.> Import Bookmarks > \[choose the
bookmark file\].*
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. 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.