We’ve been doing UCSC Genome Browser training workshops for a decade now. We’ve seen all sorts of situations–from places that had terrific bioinformatics and IT support, to places where the attendees had no idea if anyone provided support at their institution. Ironically, sometimes the places with little support were big-name research places where all the support was aimed at, or associated with, certain high-profile labs, and not the average researcher or post-doc. We have also seen places where although there was support, it was so hostile and dismissive that we could understand why the researchers didn’t seek them out. So when we went in, often people would deluge us with questions about problems they were having working with their own data.
Frequently a problem they were having was being able to incorporate their own data into a viewable and explorable way with other tools, where they could look at the deep context of genome annotations with their data. Over the years the options got better and better to do this with the UCSC tools: custom tracks, sessions, then hubs. But one problem still remained: some people couldn’t put their data over the intertubz–for a variety of reasons.
In some cases they had patient data, and HIPAA or grant agency privacy compliance issues, that restricted them to working behind their firewall. Sometimes their data sets were so huge they couldn’t get it loaded without timing out. Some places had the capacity to install a local UCSC mirror, but many didn’t. But UCSC has now solved this problem as well. Using their new Genome Browser in a Box (GBIB), you can download an installation of the UCSC Genome Browser to your own computer, use your own files, and they never have to leave your laptop or your firewall. You have your own personal mirror site. This might be a great solution for some folks at small companies too.
To accomplish this, you use a tool called VirtualBox to set up a virtual machine on your computer, you pull down the UCSC components, and you are ready to roll. I have an older and under-powered computer and it worked fine for me. It also is supported on Windows, Mac, or Linux, so it should serve most people.
This week’s video tip-of-the-week is a quick introduction to that setup. Although there is a paper already (below), good documentation (linked), and the ever-helpful mailing lists at UCSC, I thought some folks who were less likely to seek out (or have access to) the help might benefit from a walk-through of this process. I show where and how to get the GBIB, an overview of the steps, and then illustrate how this runs on my computer. You also get the benefit of my mistakes–I did testing for this before it was released, and I had installation issues, so I highlight where to get the help with that (Pro-tip: I should have printed the documentation before installing–it was all in there. And don’t forget to check the “troubleshooting” section at the end.).
So if you’ve wanted to load your own data in to the UCSC Genome Browser and use the suite of tools there to visualize and query–but haven’t been able to–give the Browser in a Box a try.
You can learn more about the concept and the implementation from the UCSC blog, see announcements, and a press release with a sweet photo of some members of the terrific team who delivered it. And, of course, the publication below.
In this overview video, I don’t go into more detail on how to use the browser–with your own mirror you are really using the same features that our regular training materials cover–the introduction to the browser and the advanced tools features are mostly the same.
Note: “GBiB is free for non-commercial use by non-profit organizations, academic institutions, and for personal use. Commercial use requires purchase of a license with setup fee and annual payment.” At OpenHelix we have a contract to do general training and outreach, we do not benefit from any license fees associated with the UCSC browser. Checking your status for licensing GBIB or the required tools is in your hands.
Get the Genome Browser in a Box at their Store: https://genome-store.ucsc.edu/ This has the system requirements detailed as well.
GBIB help (print this to help you with the installation): http://genome.ucsc.edu/goldenPath/help/gbib.html
Haeussler M., B. J. Raney, A. S. Hinrichs, H. Clawson, A. S. Zweig, D. Karolchik, J. Casper, M. L. Speir, D. Haussler & W. J. Kent (2014). Navigating protected genomics data with UCSC Genome Browser in a Box, Bioinformatics, DOI: http://dx.doi.org/10.1093/bioinformatics/btu712