Category Archives: Workshop or Webinar

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


World Tour of Genomics Resources II, webinar recording available

worldtourIIpreviewQuick update: the recent webinar we delivered, “World Tour of Genomics Resources II”, is now available as a downloadable recording. Access it here. There’s a short video preview there, but the whole thing is about an hour long.

If you want the slides and the handout with the list of resources, those are available in our previous post:  World Tour of Genomics Resources II, webinar follow-up post. We are going to convert this into a regular tutorial suite with a professional recording soon, and it will be available in our catalog then.

World Tour of Genomics Resources II, webinar follow-up post

worldtourIITypically when we do a webinar, we create a companion blog post for further discussion that we might not have been able to do in the webinar session. You might also try out the sites I talk about and come back with comments or questions. Or for folks who couldn’t make it, but later will watch, and have things they would like to discuss.

Also, it gives me a place to leave the slide handouts and the link document that go with this webinar. If you are seeing this on Thursday before the session, there’s still time to sign up: .

Slide handouts: OpenHelix_WorldTour2_handouts [PDF]

List of resources:  OpenHelix_WorldTour2_exercises [PDF]

Access our training material suites, or search for our training or tips:

Eventually the recording of the webinar will become available, and we’ll let you know. And soon we’ll turn the whole package into one of our regular tutorials suites that you can access as a movie and full script, slides, or exercises. We’ll keep you posted on that as well.

Also: if you have other tools you like, let us know! We’ll keep updating our collection and we would like to include other publicly-available resources that are useful to researchers.

[This post replaces our "What's the Answer?" post this week. Regular posting returns next week.]

Webinar this week: World Tour of Genomics Resources II

worldtourIIOne of our really popular seminars has been the “World Tour of Genomics Resources“. One time we gave it at the NIH they had to lock the room because we had hit capacity–in a pretty decent sized room that had been reserved for us. But our goal with the talk is to give a lightweight overview of a whole bunch of handy tools that you might not know about–that are provided by teams all around the world. For example–one of my favorite tools is from the Slovak Republic. Who knew, right?

Anyway–I’ve updated the World Tour with some new features and aspects since the last one. Some of the tools are the same, because they are core tools that everyone ought to know about. But others are new since the last one.

If you want to join us for the webinar (or if you can’t make it and want to access the video later), sign up here: World Tour of Genomics Resources II. It is this Thursday March 5, 1pm ET US. We’ll also make the slides and the list of tools available afterwards.

Click here for the time in other zones.


OpenHelix to exhibit at TRICON

OpenHelix will be exhibiting at the International Molecular Medicine Tri-Conference (MMTC or TRICON) at booth 129, February 16-18. While onsite at the Tri-Conference, we invite you to demo OpenHelix and not only learn how to enable more effective research, but receive a Starbucks gift card for completing the demo.

The 22nd International Molecular Medicine Tri-Conference is the industry’s Preeminent Event on Molecular Medicine, focusing on Drug Discovery, Genomics, Diagnostics and Information Technology. Spanning six days this year, the Tri-Conference includes an expanded program that includes 6 symposia, over 20 short courses, and 17 conference programs.

OpenHelix provides over 100 tutorial suites on popular and powerful bioinformatics and genomics tools. Each tutorial suites includes 30-60 minute tutorials highlight and explain the features and functionality needed to start using a resource effectively. The tutorial suites also include PowerPoint slides, handouts and exercises to save time and money in teaching others.

An OpenHelix subscription to the tutorials enables quicker and more effective research at your institution through more efficient use of the publicly available tools to access biological data. Join some of the best universities, research institutions, and biotech companies in training scientists on how to use these critical tools.

To schedule your 5 minute demonstration of the OpenHelix site and tutorial suites (and receive a Starbuck’s gift card), email Scott Lathe or call (425) 442-0322. We will be at booth 129 in the Tri-Conference Exhibit Hall.

GenoCAD webinar this Thursday, March 27

GenoCAD_logoAlthough it’s already posted in our news feed, I just wanted to add a reminder about our upcoming webinar on GenoCAD: open-source computer-assisted design software for synthetic biology. You can see the time and registration details here:

Free “Introduction to GenoCAD” Webinar presented March 27th

If you want to download the slides beforehand (so you don’t have to write everything down), you can access the slides and slide handouts for the Introduction here:

But in case you can’t make it for schedule reasons, you can still access the same materials from our web site on our GenoCAD suite pages. You can watch the video, download slides and handouts, and also try out the accompanying exercises.

There’s also a second tutorial with more advanced topics, and you can watch that video or access associated training materials for that version too:

We’ll also leave this post open for questions from the webinar–if we don’t have time to get to the issues we’ll tackle them here. Or if you go off and try some things yourself, and come up with something else you want to know or get stuck, we’ll get you the answers or guidance.

If you are the type to want some publications to read to better understand the resource, be sure to check out the GenoCAD team’s page with many references that will help you to understand the foundations of the development and features, and their directions going forward.

Wilson M.L., Hertzberg R., Adam L. & Peccoud J. (2011). A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD., Methods in enzymology, PMID:

Building computational skills for women in science

get trainingIt’s really crucial for scientists of all stripes to have some computational skills in their toolbelts. In genomics, the deluge of data that needs to be sorted, sifted, and analyzed is not going to stop–so it’s even more urgent that everyone gets some comfort and capability to work with the data, do some scripting to solve some issues you might have, and assess the tools you might want to be using.

For various reasons, women in science may not have pursued much coding. But there are new efforts to bring women researchers up to speed on some of these skills by the Software Carpentry team. There’s a workshop coming up in Boston in June that is a great opportunity if you’ve been thinking about tackling some of the basics.

Women in Science and Engineering (Boston): Jun 24-25, 2013

Click that link to access the registration page. It’s only $20 for two days. It’s a bargain.

Bostonians: if you don’t need the skills, send your students. Tell your department. Put up a flyer on the bulletin board.

Rare photo of me in the wild….

Of downtown Boston, at Tufts Medical Center, singing the praises of IMG and the Integrated Microbial Genomes resources.

I love workshops that only require a trip on the Orange Line.

Today we were doing the World Tour of Genomics Resources. Tomorrow it is UCSC Genome Browser (intro + advanced), and Thursday ENCODE. So if you want to workshop vicariously you can check out all of our tutorials on those. The slides, handouts, and exercises are all over there for you to download if you’d like.

As much as I love the online training and webinars and all, you really do get important information about the needs of folks in the room that you just don’t really get from the intertubz, and I do like to do the material live.

UCSC / ENCODE webinar follow up post

We’ll be having our July 24th UCSC – ENCODE webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If you aren’t able to make the webinar today, don’t worry. In the near future, a movie with the exact same material will be available with the slides, and exercises tutorial suite–we’ll announce that on the blog when it’s ready. For now you can download the slides here.

You can also sign up to be informed of future webinars coming up other topics.

ENCODE data in the UCSC Genome Browser webinar Tuesday

We’ve got a webinar coming up Tuesday July 24 exploring our brand-new “ENCODE in the UCSC Genome Browser” materials. We are preparing the accompanying movie, but it’s still in our studio right now. So this is your first chance to see the new materials.

To register, go here:

This webinar explores how to identify and explore many of the human data types in the UCSC Genome Browser that have come through the ENCODE project. If you aren’t familiar with the ENCODE project–or need a refresher–you can see our ENCODE Foundations tutorial suite. That’s freely available because it was sponsored by the UCSC ENCODE team. It’s not required for the new tutorial, but it would give you some background on the project.

You can access our webinar slides here (zipped):

We’ll announce when the full suite of materials is available (very soon we hope!).

After the webinar, we’ll also field questions here on the blog in a follow-up post if we didn’t have time or the answers need links and further detail, or if you go away and try out some things and have other issues that arise you can ask us later.

Quick links:

Webinar registration:

UCSC Genome Browser:

ENCODE portal at UCSC:

ENCODE project pages at NHGRI: