UCSC Genome Bioinformatics

Video Tip of the Week: Introduction to the UCSC Genome Browser

UCSC Genome BioinformaticsThis week’s tip is quite multi-media. There’s a video, as required. But there’s a traditional published paper format, too. And there’s also the free training slides and exercises from us, sponsored by the folks who create the UCSC Genome Browser. So if you prefer audio, graphics, or text–we’ve got it all in this week’s tip.

For years we’ve been doing the UCSC Genome Browser online training suites. And those materials are still available for everyone to see. But I know some people prefer to have someone walk through the stuff in a webinar or workshop. And if you are using our materials yourself for training others, it might help to hear how I present it “live”. For this week’s tip, here’s a snippet of the recent webinar I just did, with my most current slide set.

You can access the whole thing from our site here: http://www.bio-itworld.com/openhelix/introduction-to-the-ucsc-genome-browser-webinar/

But the main reason I’m highlighting this is because of our paper that’s recently been un-firewalled. We have this Current Protocols in Molecular Biology paper that we did a while back (first in 2009), and they asked us to update this last year. This updated version is now publicly available in PubMedCentral.

This paper was a fun paper to write. I like to do the step-by-step series. It forces me to really think like a new user, looking at the menus and the buttons and everything that someone new to the software might face. And if you are in a teaching situation, you could offer this paper to students to let them try these things out. You could pair it with either the webinar or our standard recording. And I think this multi-media strategy could be really effective in getting people to grasp the concepts, and also build their confidence with the tools.

I spent some time working through the paper to see if there were any serious differences since we submitted it a while ago. I will note that there are a few changes since we wrote this. For example, the former “Variations and Repeats” group has become “Variations” and “Repeats” as separate track groups. And “Literature” moved into “Phenotype and Literature”. But I don’t think that will trip up most users. Use that as a teachable moment about interfaces changing…. Also, of course, version numbers for dbSNP have changed. But again–most people can follow along, or even try the old version to see the differences.

Probably the biggest difference is the part with the evolutionary relationships. Now that there are 100 species instead of the prior 46 species version, a couple of things about that interface changed. Now you need to check “All species” instead. They don’t separate out vertebrates the way they used to.

Another interface change in the part with the Track Hubs will be potentially confusing. As an introduction to hubs, Bob Kuhn wrote this part that walks you through the basic structure of the setup of a hub. All of our text it still ok, but you can’t just get the URL like we had originally shown. Still, it walks you through the structure of the hubs without problems if you just type the URL instead of copying it.

So use our materials to teach yourself, or to teach others. We hope this offers different ways that will work for everyone.

Quick links:

UCSC Genome Browser: genome.ucsc.edu

UCSC Intro Webinar: http://www.bio-itworld.com/openhelix/introduction-to-the-ucsc-genome-browser-webinar/

UCSC Intro Tutorial suites (video, with our free slides + exercises): http://www.openhelix.com/ucscintro

UCSC Advanced Tutorial suites (video, slides, exercises): http://www.openhelix.com/ucscadv

Reference:

Mangan ME, Williams JM, Kuhn RM, & Lathe WC (2014). The UCSC Genome Browser: What Every Molecular Biologist Should Know Current Protocols in Molecular Biology., 107 (19.9), 199-199 DOI: 10.1002/0471142727.mb1909s107

Disclosure: These tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.