Customizing Your Digital Research Environment with Genome Browsers, #BioIT15

openHelixLogoEvery time we do a workshop on genome browser tools and other associated resources, we find that there’s someone who’s shocked to discover how much they didn’t realize was underneath the interface. One of my favorite responses was a workshop at a midwestern medical school, where a guy came up to me after the talk and said that he’d been using the UCSC Genome Browser for 10 years, and he had no idea there was so much more to it.

We’ve expanded our workshop to cover that and a lot of other tools that researchers have been really pleased to learn about. Some are big projects, some are smaller but really handy items that save researchers time and help them to communicate their own research to others.

Here’s the description, and this particular workshop will run at Bio-IT World soon. If you are going to that conference, you can register for it over there. But we can also take it on the road if you are interested in sponsoring one at your site.

W12: Customizing Your Digital Research Environment with Genome Browsers

Tuesday, April 21, 2015 | 12:30 – 4:00 pm

Even the most widely-used genome browsers have features that you might not be aware of. This interactive workshop on using popular web-based tools to customize your digital research environment will help you to become adept at using the UCSC Genome Browser and other browsing options.

One segment of the material will be an introduction to the fundamental visualizations and filtering strategies available with the UCSC Genome Browser framework. We will also introduce basic custom tracks to establish the foundation for creating your own data views in the UCSC Genome Browser from custom queries, or from novel tracks of your own data. We’ll describe the availability of the new Genome Browser in a Box that you can set up on your own computer to have a local copy of the UCSC Genome Browser to work with.

We’ll continue to briefly explore ways to visualize your own data in other browsers and analysis tools, including IGV and Galaxy. And we’ll touch on a variety of other tools that will help you to visualize, explore, and present your data in other ways, such as set analysis with UpSet, and displays of domains and mutations on your sequences of interest with handy tools like DomainDraw, FancyGene and MutationMapper.

No prior experience with the UCSC Genome Browser, or programming skills, are required. Free training materials that you can use to train your teams will be provided.

Topics to be Covered:

  • Key features for understanding visual representations will be examined
  • Learn to set up custom views to focus on your features of interest
  • Explore ways to load your own data to enhance your setup