Tag Archives: sessions

UCSC Genome Browser “Sessions” minor change

When we began doing training on the UCSC Genome Browser nearly a decade ago, we were going around and telling people about all these cool things they could do to show what they wanted in a genomic region. And they began to ask us: Can I save this view if I like it? We heard that over and over, and gave that feedback to UCSC.

And lo and behold: Sessions! The UCSC team created a way to store the filters, menus, tracks, regions–to show exactly what you wanted, and reload them later for yourself. Or you could get a URL to share with others. This was a HUGE hit as we went around doing more trainings.

Here’s our first announcement about that–from 2008: Oh, could you take a look at this? Browser sessions.

I use this all the time now. It’s great for training, blogging, and other conversations with people. There’s a few genomic regions I’m scientifically interested in, and sometimes I reload those and look at new SNPs or ESTs or other data that might have come in (and next week’s Tip of the Week will cover another new data type!).

If you haven’t used Sessions, check them out. We mention them in the intro training–and mention that you have to create a login in the wiki system. But just now I got a mailing list notice that they have changed that slightly–it’s not the wiki login now, it’s a new system. But not to worry–I just tested it, and it’s true: all my sessions are there, and it was no problem to just use the new login interface. Remembered all my stuff.

Here’s the announcement:

If you have ever created or used Sessions in Genome Browser, then you have signed into the website. (If you don’t know what a Session is, they are useful for saving or sharing a snapshot/configuration of the Genome Browser. Read more about them here: http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html).

In the past, the sign-up process was handled by our wiki site: http://genomewiki.ucsc.edu. Today we released a new sign-up method and are discontinuing our reliance on the wiki site. Other than a few minor changes to look-and-feel of the Session page, this change will be transparent to you. You will continue to save, share, and load saved sessions as before. All previously-saved sessions are still available under the same username. Your username, password and email addresses are all the same as they were before the change.

The current Media-wiki server at http://genomewiki.ucsc.edu will continue to serve as a forum for users to share knowledge and ideas.

As always, if you have difficulties with Sessions or anything else on the website, do not hesitate to ask our help desk at genome@soe.ucsc.edu.

To see the intro training that includes the session piece (freely available as it is sponsored by UCSC): http://openhelix.com/ucsc

Saving your genome views: Ensembl (and UCSC Genome Browser, others)

In the latest update of Ensembl, the developers added the ability to save configurations. This allows you to set your  track views and analysis to a specific configuration and load that configuration at a later time. The blog post linked previously (or here) explains the steps to creating your own configurations you can save and return to. In the future they will be adding the ability to share your configurations with colleagues and other researchers.

UCSC has a similar function they call sessions. You can read more about it here on our blog or go to the sessions user guide at UCSC.

As far as I know, NCBI’s Map Viewer does not have the same functionality (please correct me if I’m wrong).

GBrowse has the ability to save sessions, but since it is an open-source program, it will depend on the specific installation on whether that function is available.

Mouse KOMP, all over the browsers

An email from the MGI mailing list alerted me to some interesting new data on the browsers. The mouse KOMP project is generating knock-out mouse ES cells for every gene in the genome (well, that’s the goal anyway). This means you will be able to buy off-the-shelf mouse knockout cells for lots of regions you might want to study. You can grow ‘em up, and then breed ‘em with other mutants. You can characterize them in your favorite developmental stages and tissues. What a terrific reagent collection. In fact, if I was a post-doc, I would be looking for very interesting genes in this data set to pursue. You could start a whole career characterizing some of these beasts.

The email from MGI says:

The NIH funded Knockout Mouse Project (KOMP) is in full swing and reagents (vectors, ES cells, mice) from this project are becoming available to the research community.

Find out more about the KOMP project, which genes are being targeted, and which genes have reagents available for distribution by visiting the Knockout Mouse Project Data Coordination Center at http://www.knockoutmouse.org.

The UCSC genome browser (http://genome.ucsc.edu) now has a “KOMP Gene” track that shows which mouse genes are being targeted by the KOMP project. The tracks are linked to the KOMP Data Coordination Center site for the most recent information on project status and reagent availability.

KOMP gene information is also available in the Ensembl genome browser for mouse (http://www.ensembl.org/Mus_musculus/index.html) and will soon be available on the MGI Mouse Genome Browser (http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_current/).

Of course I went looking for some examples. I found a couple to show you on the UCSC Genome Browser and I created sessions to share. If you would like to look at tracks that indicate the region of the knockout you can see this one that indicates the gene Xpr1 is knocked out and ready for you–see the bright green bar track in about the center of the page.

Another example is March4. Here blue and yellow tracks indicate a different status at the 2 groups performing the knockouts. Blue is “not started/on hold” and yellow is “in progress” according to the code on the details page (click the blue or yellow track to see that color code info on the description page).

Although it says the data is also in Ensembl I couldn’t find it–I have a query in to the help desk on that. Will let you know what I learn.

Edit: word back from ensembl = “KOMP data is in a track along with other KO alleles (EUCOMM and NorCOMM). In Ensembl it is called “Alleles”, available in the drop-down list in contigview.” But I’m looking in those same regions as I know data exists from the UCSC stuff and I still don’t see anything. You can go to those URLs but you’ll have to open the DAS sources menu and check the “alleles” box. March4 in ensembl. Xpr1 gives me an error message in the track (Error retrieving KO_vectors features (Can’t connect to the host!). Second attempt said No KO alleles in that section.

And it will be on the MGI GBrowse soon, too. I’ll try to find a sample of that when it is available too.

Oh, could you take a look at this? Browser sessions.

Have you found yourself wanting your colleagues to look at some region of the genome, the way you have it set up on your browser at that moment? Yes, you changed some colors and customized the display a bit. You picked exactly the stretch you want to show. But thisthey have to see this!

I found myself wanting my colleagues to look at that stretch of genes implicated in that autism research from the other day. So I went to the paper and found figure 1 where they have the list of genes and the region indicated, and went over to the UCSC Genome Browser to look for myself. And I could just tell you to go over to UCSC. Or I could show you my saved session–where I put that region in focus and could have set up the display any way I wanted. Follow me over the flip to learn more, and to view my session. Those duplications at the end are really apparent here–check out the BOLA2 on each end. Same with SULT1A3. And others. Isn’t that curious and intriguing?

As we were doing trainings around the country on the UCSC Genome Browser and explaining to people how great it was to be able to customize their view with filters and track choices, people were asking if they could save all that. And yes–the browser remembers where you were last, so it is still there. But if there was one view you wanted to create regularly and go back to, or you wanted to share that particular view with your colleagues, UCSC created the Sessions mechanism to enable this.

When you start working around in the Genome Viewer, you will find yourself in a genomic region like this one. At the top of the browser page, in the blue navigation line, you can see the option for Session. If you click that you will be able to save your current exact view, and you will have the option of loading that in the browser or generating an email with that link. The sessions are stored and you can go in and use them later, and other people can load them later. This is much easier than dragging your colleague over to your computer at exactly the moment you need them. Especially if your colleague is not in your department, or even your country! It might also be handy for teaching or training like we do–you can set up a specific region that you know everyone is on at the same time. And for those of you who are the local help desk–answering questions from your colleagues about how to look at stuff in the genome browser–voilà. You look great!

It will require a login and password for the UCSC Genome Wiki. But once you have that you are ready to go.

This feature was described in the 2007 news, [edit: and in the paper below] and the details are:

16 February 2007 – New Browser Session-Sharing Function Available

We are pleased to announce the release of a new session management functionality in the Genome Browser, which allows users to save and share browser sessions.

Users are now able to configure their browsers with specific track combinations, including custom tracks, and save the configuraton options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for one year after the last access, unless deleted. Custom tracks persist for at least 48 hours after the last time they are viewed.

The new feature may be accessed via the “Sessions” link in the top blue bar in any assembly. To ensure privacy and security, users must login to the genomewiki site and create a username and password. Individual sessions may be designated by the user as either “shared” or “non-shared” to protect the privacy of confidential data.

To avoid having a new shared session from someone else override existing Genome Browser settings, users are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session.

The Sessions feature was written by Angie Hinrichs of the UCSC Genome Bioinformatics Group and released with the assistance of Kayla Smith and Robert Kuhn.

Edited to offer citations for the research components:

1. Autism research paper: Weiss, L.A., Shen, Y., Korn, J.M., Arking, D.E., Miller, D.T., Fossdal, R., Saemundsen, E., Stefansson, H., Ferreira, M.A., Green, T., Platt, O.S., Ruderfer, D.M., Walsh, C.A., Altshuler, D., Chakravarti, A., Tanzi, R.E., Stefansson, K., Santangelo, S.L., Gusella, J.F., Sklar, P., Wu, B., Daly, M.J. (2008). Association between Microdeletion and Microduplication at 16p11.2 and Autism. New England Journal of Medicine DOI: 10.1056/NEJMoa075974 .

2. UCSC Genome Browser paper: Karolchik, D., Kuhn, R.M., Baertsch, R., Barber, G.P., Clawson, H., Diekhans, M., Giardine, B., Harte, R.A., Hinrichs, A.S., Hsu, F., Kober, K.M., Miller, W., Pedersen, J.S., Pohl, A., Raney, B.J., Rhead, B., Rosenbloom, K.R., Smith, K.E., Stanke, M., Thakkapallayil, A., Trumbower, H., Wang, T., Zweig, A.S., Haussler, D., Kent, W.J. (2007). The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research, 36(Database), D773-D779. DOI: 10.1093/nar/gkm966