Sessions User's Guide
| ### Table of Contents: Introduction Some Simple Examples Creating a Session Session Details Sharing Sessions Editing an Existing Session Displaying Your Own Tracks in a Session Deleting a Session Lifespan of a Session Questions and feedback on this User's Guide are welcome. User questions and answers on Sessions and other topics are available in the Genome mailing list archives. Search the Genome mailing list archives: |
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 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. |
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 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: 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.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. Example 2a: `http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit& hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1`. Example 2b: `http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit& hgS_otherUserName=Example&hgS_otherUserSessionName=hg18_HAR1_zoom`. 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` |
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 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. |
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: 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. |
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 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: 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 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. 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. |
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: Custom Tracks Genome Graph 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. |
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
| 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. |