Sessions User's Guide
 

Table of Contents:

Questions and feedback on this User's Guide are welcome.

User questions and answers on Sessions and other topics are available in the Genome Browser mailing list.


  Introduction
 

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 will not be expired, however, we still recommend that you keep local back-ups of your session contents and any associated custom tracks. BLAT result 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 create an account and log in before using the session manager.

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.


  Some Simple Examples
 

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.

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: Example
    session name: hg17_chr2_primate
    Click 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.
  • 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.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:


  Creating a Session
 

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 My Data pulldown in the top blue navigation bar. Follow these steps to save your session:

  • Log in to the Genome Browser. To ensure privacy and security, you must create an account and/or log in to use the Session tool. 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.

Saved sessions will not be expired, and should persist until you delete them. However, it is still recommended that you keep local back-ups of your session contents and any associated custom tracks.


  Opening a Saved Session
 

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:

  • Session name. Click the session name to view it in the Genome Browser.
  • View/edit details. Click the details button to edit the session description and view sessions details such as creation date/time, assemblies with custom tracks and more.
  • 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.
  • Post in public listing: Check this box to add your session to the list of Public Sessions. Sessions in the listing will be availble to be loaded and viewed by the world.
  • Email. Click this link to email this session to a colleague.

  Session Details
 

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.


  Sharing a Session
 

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 shared and must be explicitly changed to non-shared status.

Shared sessions can be opened by other Genome Browser users to whom you've provided one of the following:

  • 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
Sessions which you've added to the list of Public Sessions will available to the world. Note that unless you've added them to this list of Public Sessions, 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.

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 five ways to let others know about your saved sessions:

  • Save the session URL. Immediately upon saving a new session, the top of the page offers a Browser hyperlink. Additionally, each session entry in the My Sessions list has a Browser hyperlink. Click either Browser link to open the Genome Browser with the session loaded. You can obtain the URL of the Genome Browser page by capturing the Browser hyperlink via right-click before you proceed to the Browser graphical view. You can then store the URL, create a bookmark or share the link 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.
  • List it on the Public Sessions page. The "Public Sessions" tool allows you to post and share your exciting and interesting Browser snapshots with the world. After having saved your session, you can add it to this public listing by checking the box in the column under "post in public listing?"

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.


  Editing an Existing Session
 

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.


  Displaying Your Own Tracks in a Session
 

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 associated with a saved session will not be expired. BLAT results always have a lifespan of 48 hours, even if they are part of a session.


  Deleting a Session
 

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.


  Lifespan of a Session
 

Your saved sessions will not be expired and will available you (and others if you share them) until you delete them. We have discontinued our previous policy of removing saved sessions and associated custom track data after four months. However, note that the UCSC Genome Browser is not a data storage service; please keep a local backup of your session contents and custom track data.


  Session Gallery
 

The Session Gallery is a collection of track views that help highlight viewing different topics in the browser. The sessions in the Session Gallery were created in the browser and then saved to a local file, which was then uploaded to an online location. This allows creating a single link, such as http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=U, where U is the URL of the session file, e.g. http://www.mysite.edu/~me/mySession.txt, enabling users to maintain external control of the content file for easy update.