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 |  | The Session 
   tool allows you to configure your browser with specific 
   track combinations, including 
   custom tracks, 
   and save the configuration 
   options. Multiple sessions may be saved for future reference, for comparing 
   different data sets, or for sharing with your colleagues.  
   Saved sessions persist 
   for four months after the last access, unless deleted. 
   Custom tracks persist 
   for at least 48 hours after the last time they are viewed.
   The creation date of a session can be viewed in the Session
   Management menu. This date only reflects the inital creation of the
   Session and is not updated when sessions are edited. Descriptive 
   text can also be added to a session in the 
   Session Details menu.
    This feature may be accessed via the Session link in the top 
   blue navigation bar in any assembly. To ensure privacy and security, you 
   must log in to the UCSC 
   Genome Wiki 
   website and create a username and password before using the session manager. 
   The Session tool makes use of the built-in security of the wiki tool. Individual sessions may be designated as either 
   shared or non-shared 
   to protect the privacy of confidential data. 
   To avoid having a new shared 
   session from someone else override your existing Genome Browser settings, 
   you are encouraged to open a new web-browser instance or to save existing 
   settings in a session before loading a new shared 
   session. Note that not all of the Genome Browser 
   mirror sites 
   have all of the session features enabled. This User's Guide provides a few examples that introduce the features of
   the Session tool, followed by detailed directions on creating, saving, 
   modifying and sharing sessions. |  |  
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 |  | This section contains some example sessions that demonstrate the 
   use of the Session tool. To enable you to view these sessions, we have
   created a user account with the name Example in 
   the UCSC Genome Wiki.
    Example 1
 This example shows the primate (chimp and rhesus) nets 
   for chromosome 2 in the hg17 human assembly — the primate 
   chromosome that fused in humans. We first configured our browser view with
   the desired settings, and then saved the session so that we 
   could share it. We named our session hg17_chr2_primate. There are several ways for you to view this session:
    
   Manually load and open the session. 
    Open the Session 
    tool. In the Session Management section under the
    Load Settings heading, enter this information:
    
    user: ExampleClick the submit button next to the session name box to load the 
    session.  To view 
    the session in the Genome Browser, click the Genome Browser 
    link in the top blue navigation bar.session name: hg17_chr2_primate
Open a session link sent by email. After we created and saved this
    session, we could have clicked the 
    Email link to automatically send a message to one or more 
    recipients with the following contents and clickable link:
    
     Here is a UCSC browser session I'd like to share with you: 
     http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Examples&hgS_otherUserSessionName=hg17_chr2_primate. 
    By clicking this link, you can open the session in your browser.Open a session from a local file. 
    Alternatively, if we had saved the browser settings to a local file, we 
    could have simply provided the location of that file for you to
    load into your browser to view our session. Click 
    here to see such a settings file. 
    This method works best when the file is in a location that you can 
    access from your own computer or network. For this example, you can copy 
    this file and paste it into a file on your own machine, 
    then load it into the Session tool.
   Open a session from a URL.
    Because you do not have access to our file system where this session 
    file resides, it will be easier for you to load it using a URL. To do 
    this, open the Session 
    tool. In the Session Management section under the
    Load Settings header, enter the URL where this file is located:
    
    http://genome.ucsc.edu/goldenPath/help/examples/session_example1.txt
    Then, click the submit button to load the session settings. 
    To view the session in the Genome Browser, press the Browser 
    link in the Updated Session section. Example 2
 This example shows the Human Accelerated Region (HAR1) in the 
  hg18 assembly. Eighteen differences exist in a region of 118 bases between 
  human and all other mammals extending back to the chicken. The two 
  sessions in this example show the same browser position at 
  two levels of detail: Example 2a is zoomed out; Example 2b
  is zoomed in.
   To view these sessions in your browser, you can use any of the methods
  described in Example 1:
   
   Manually load and open the session. 
   
    Example 2a:user: Example
 session name: hg18_HAR1
Example 2b:user: Example
 session name: hg18_HAR1_zoom
Open a session link sent by email. 
       
  Open a session from a local file. 
    
     Example 2a: Copy the contents of this 
      file to a file on your own 
        machine, then load it into the Session tool.
     Example 2b: Copy the contents of this 
      file to a file on your own
       machine, then load it into the Session tool.
     Open a session from a URL.
    
     Example 2a: Paste this URL into the Session tool: 
      http://genome.ucsc.edu/goldenPath/help/examples/session_example2a.txt
     Example 2b: Paste this URL into the Session tool: 
      http://genome.ucsc.edu/goldenPath/help/examples/session_example2b.txt
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 |  | It is easy to create a session to save or share. Simply configure the 
   Genome Browser as you wish, then navigate to the Session tool by clicking on
   the Session link in the top blue navigation bar. Follow these steps
   to save your session:  
    Log in to the Genome Wiki. To ensure privacy and security, you must 
    log in to the UCSC
    genome wiki
    website and create a username and password. You will be prompted for this
    information the next time you sign in to the Session tool. After creating
    your wiki account and logging in, you will be returned to the Session 
    tool automatically. You will not have to repeat the login step unless you
    sign off from the Session tool or close your Genome Browser. Create a named session. Scroll down to the Save Settings 
    section of the page.  Type a name into the Save current settings as 
    named session box.  Choose whether or not you would like to 
    share your 
    sessions with others.  If the allow 
    this session to be loaded by others box is checked, anyone will be 
    able to view your Genome Browser settings (including your custom tracks) 
    if you provide them with your user and session name.  Note that your 
    session is not automatically available to the general public if you
    choose this option: you must provide the user and session name to other 
    individuals for them to view it. This helps to ensure the confidentiality 
    of your private data.  
    After naming the session and choosing your sharing option, click the 
    submit button. Your session will then be listed by name 
    under My Sessions.Save session settings to a file. Alternatively, you can create a 
    file from your session settings that
    can be saved to your local machine or posted to a URL for 
    access or sharing.  To do this, go to the 
    Save Settings section.  
    Type a name into the Save current settings to a local file 
    box.  Click the submit button to save or display the file.
    The session will be saved in plain text (ascii) format by default. To select
    a compressed format, select one of the options from the file type
    returned menu before clicking submit. If you simply
    wish to preview the contents of the file in your browser window, leave
    the file name blank and click submit.
    After you save a session, it will be 
   available to you for four months. |  |  
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 |  | When you save a session, it is added to the My Sessions list on 
   the Session page. Each session entry is listed by name and offers the 
   following options to open, share, and manipulate it:
    
   Use this session. Click this button to load the session as
   your current session without launching the Genome Browser. This allows you to
   perform other configuration tasks on the session before opening it in the 
   browser. To launch the Genome Browser using this session, click the 
   Browser link.
   Delete the session. Click the delete button to 
   permanently remove this session from the list.
   Share with others: Check this box to allow others to access this
   session. By default, this option is unchecked, which limits access to only
   the session owner. 
   Browser. Click this link to open the Genome Browser using these
   session settings.
   Email.Click this link to email this session 
   to a colleague. 
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Each session has an associated details page that you can click into from the
Session Management
menu. The Session Details menu allows you to edit the Session Name, 
to add descriptive text and to change whether or not the session is shared with others.
Like the Session Management menu, if you click "use" that session will be loaded
as the current session and if you click "delete" the session will be deleted. The 
"Created on" date reflects the date that the session was originally created and will
not be updated to reflect any edits. 
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   Shared vs. Non-shared Data When you create a session using the Session tool, you may designate it as 
 either shared or non-shared. By default, new sessions
 are created as non-shared and must be explicitly changed to shared status. 
  Shared sessions can be opened by other Genome Browser users to whom you've
 provided one of the following:
  
 Note that your shared sessions will not be available in a general way to 
 other Genome Browser users; they will need at least one of these access 
 methods.the user name and session name of the saved session
 access privileges to a local file that contains the saved session 
 information
 the URL of a web-accessible session settings file
  If you choose to keep your session private, other users of the Genome 
 Browser will not be able to access your data or browser configuration. Any 
 confidential data or locations of interest that you are working with will be 
 safe from viewing by others.   The most secure way to control your session is to save the settings to
 a local file, then deny access to that file by others. Sharing Your Session with Others
 There are four ways to let others know about your saved sessions:
   
  Bookmark the session. Each session entry in the My 
   Sessions list 
   has a Browser hyperlink. Click the Browser 
   link to open the Genome Browser with that session loaded. Bookmark the 
   URL of the Genome Browser page that is displayed, then share the bookmark 
   with others. 
  Email a session link. Each session entry in the My 
   Sessions list
   also has an Email link. Click this link to automatically 
   invoke your email tool with a message containing the Genome Browser URL, 
   which you can then send to others.Share a session settings file. If you have saved your settings to a
   local file, you can give others access to the file, or email the file to them
   as an attachment and instruct them to load it using the 
   Session tool.Share a web URL. If you have saved your settings to a file on a 
   web server, you can provide a link like this to others: 
   
   http://genome.ucsc.edu/cgi-bin/hgSession?hgS_doLoadUrl=submit&hgS_loadUrlName=MyUrl
   where MyUrl is the URL of your settings file, e.g. 
   http://www.mysite.edu/~me/mySession.txt. In this type of 
   link, you may 
   replace "hgSession" with "hgTracks" 
   to proceed directly to the Genome Browser. Opening a Shared Session
 If you open a shared session while viewing the Genome Browser, 
 it is possible to lose all of your own browser settings.  That is, 
 the settings for the newly-opened session will take precedence over your
 existing settings and will replace them.  If you wish to preserve your original
 settings, you should first save your own settings as a session before opening 
 a new session, or open a new tab or window in your internet browser before
 loading the new session. There are four ways to open a shared session, depending on what 
 information you have about the session. The instructions below assume that you
 want to replace your current session the new session. Be sure to preserve your
 original session first if you don't want to overwrite it.
  
  Open a session from an email link. If you receive an email message 
  with a link to a colleague's shared session, simply click on the link to
  view the Genome Browser with the session settings.  Open another user's session. If you know the name of another user's
  shared session you can type in the user and session name in the "Restore Settings"
  section and click "submit". This will generate an "Updated Session" message 
  and you can click on the Browser link to load the browser with the settings saved
  in this session.Open a session from a settings file. Open the Session tool, 
  then scroll down to Load Settings in the Session Management
  section. Type in the name of the settings file, or click 
  Browse... to find the file on your computer. Click
  submit to display the Genome Browser using these session
  settings.  Open a session specified by a URL. Open the Session tool,
  then scroll down to Load Settings in the Session Management
  section. Type in the URL in the Load settings from a URL
  box, then click submit to display the Genome Browser using
  the new session settings.  Note that you 
  may also choose to save a copy of your colleague's session as your own. Any
  changes you make to this newly-saved session will not be seen by your
  colleague until you resave it and share it with them. |  |  
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  | Editing an Existing Session |  
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 |  | It's easy to make changes to an existing session.  Reconfigure
   the Genome Browser as you wish, then resave the session with the same name.
   The Session tool will warn you that you are about to overwrite an existing 
   session.  You can also edit any descriptive text associated with your session 
   as well as whether or not the session can be shared in the
   Session Details menu. Note that editing a session
   will not alter the creation date listed in the 
   Session Management
   menu.  If you previously shared this session with others, they will not see the
   changes until they reload your newly-edited session. |  |  
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  | Displaying Your Own Tracks in a Session |  
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 |  | In addition to displaying standard UCSC tracks in your session, you can 
   also display the following user-generated tracks:
   Before you create and save your session, be sure to upload your 
   Custom Track or 
   Genome Graph track.
   These user-generated tracks will be kept for four months from the
   time the session was last accessed.  BLAT results always have a lifespan of
   48 hours, even if they are part of a session. |  |  
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 |  | In the Session Management section under 
   My Sessions, press the delete button 
   next to the session name you would like to delete.  This will 
   permanently delete all details of the session from the UCSC server. 
   Any saved links to that session will no longer work. No other user can delete your saved sessions, even if you have provided
   access to your sessions to them.  Other users simply have a copy of
   your session. Unlike most other browser preferences, the session settings are 
   not saved in your Genome Browser "cart". Therefore, if you 
   choose to reset the Genome Browser, it will not delete your saved 
   sessions. |  |  
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 |  | Once you save a session for the first time, it will be available to you 
   (and others if you share it) for four months. The creation 
   date will also be saved and displayed in the Session Management menu. If you 
   access the session again during those four months, it will then be available 
   for another four months after the access date. So, as long as you access your session 
   at least once every four months, it will persist on the server until you 
   delete it. Note that it is possible for user-generated 
   tracks contained within sessions to expire before the session does.
   If that happens, your session will persist without those tracks. |  |  
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