So you want to run an Ensembl workshop

We think the Ensembl workshops that we offer are a brilliant way to familiarise yourself, and other people in your research institute, with Ensembl data and tools. Don’t take our word for it, over 99% of the people who attended our workshops in the first six months of 2016 would recommend them to a colleague.

Pie chart of who would recommend Ensembl workshops.

68% of participants say they are “Very Likely” to recommend our workshops, while 31% say they are “Likely” to.

So if you (and your colleagues) want to get training on Ensembl, the best option is to join the over 50 institutes a year who benefit from hosting an Ensembl browser workshop, training over 1000 people. Send us an email to find out more.

We appreciate, however, that that’s not an option for everybody. Although we do not charge fees for workshops, we ask our hosts to pick up the tab for all expenses incurred, such as travel, accommodation and subsistence. While we do our best to alleviate these costs, such as tagging together overseas workshops in a series, you may still not have the spare budget for this or may want to host workshop to a different timetable than we can support.

In this case, if you are an experienced Ensembl-user, you may consider teaching an Ensembl workshop of your own. We’d like to help. We want everybody learning about Ensembl to receive the most extensive and up-to-date training possible, and we believe that the second best way to do this (after having us do it) is with our support.

How can I teach a workshop?

All our workshops are hands-on, usually in a computer teaching room, although we can work with people bringing laptops (provided suitable WiFi and somewhere to charge them through the course). We recommend a similar set-up.

Our general style for a workshop is that we split it into modules. The modules we usually offer are:

  • Introduction to Ensembl and the Region view
  • Genes and transcripts in Ensembl
  • Data export with BioMart
  • Genetic variation data in Ensembl, including annotating your own variants with the VEP.
  • Comparative genomics: homologues and whole genome alignments.
  • The Ensembl Regulatory Build: finding features that regulate genes.
  • Advanced access to Ensembl data and viewing custom data in Ensembl

Within each module, there are three elements:

  1. Presentation, where we introduce what the data or tool is and where it comes from.
  2. Demonstration, where we have a hands-on walkthrough of finding that data or using that tool. We give out printed booklets containing screenshots that take participants through these walkthroughs. This provides a suitable place to make extra notes, and gives participants something to take away and use later. Some participants choose to join in with the walkthroughs, while others just make notes while we go through it on the screen.
  3. Exercises, where participants can practice using Ensembl to find information. These exercises build on what we do in the demonstration. During the exercises, we circulate the room, ready to answer any question that might come up. We also provide answer sheets (usually electronic only) that guide the participants on how to get the answers and what they are.

We find that combining these three elements gives the participants all the information they need, and provides a holistic learning experience that appeals to different kinds of learning style. We think this is why we consistently get such excellent feedback from our course participants.

You can see an example of a course that follows this structure, with the full set of modules, each with three elements, in our webinar course that we held in Spring 2016. You’re free to harvest the presentations (embedded as pdfs), demonstrations and exercises from that course for your own teaching, although under our Creative Commons BY licence, you need to credit us with their creation.

While we would usually have the workshop as one intensive day of learning, the flexibility of being in your home institute might mean that you prefer to have a module a day over a number of days or or one a week.

Where do I get the materials from?

As well as the webinar course I already mentioned, we have a page of walkthroughs and exercises. We use these ourselves in workshop creation, copying and pasting them together to make our courses.

We like to tailor our courses to match our participants’ interests, so will try to use exercises and walkthroughs that feature the species they’re working with. This is why our exercise page has many similar exercises and walkthroughs with different species. We recommend finding suitable exercises and demos to match your group’s interests and skills. You can also copy the process and style of an existing walkthrough or exercise for an example in a new species of interest.

Because we only update these exercises and walkthroughs when we use them, they can get out-of-date. The “Updated” column on the tables shows you for which Ensembl or Ensembl Genomes release they were last updated. If the exercise or walkthrough you’re looking at is not from the current release (check the release news section of this blog to see what’s current – note the different release numbers for Ensembl and Ensembl Genomes), then you might want to check the content to see if it needs editing at all.

If you do any updates, or make any new exercises, we’d love to hear about it. Email us your new material and we’ll add it to the page for other people to use (and maybe steal it for ourselves too).

For presentations (in pdf) and to see how a whole workshop might fit together, all of the Outreach team post their course materials online for use during and after the courses. You can see the materials from on our training pages.

Remember, if you use any of our materials, do credit us with their creation, as they are distributed under a CC BY licence.

What about website downtime?

Website downtime can be a disaster for a workshop, leaving you floundering with no way to teach. However, downtime is also an occasional necessity when we are running such a huge website and database. If you are planning on running a workshop, we recommend you get in touch to ask if there is any planned downtime. You can usually get around downtime by using one of our mirror sites, but we can advise you on this.

Similarly, if we put out a new release in the days between your preparation and workshop delivery, it can make some of your materials out-of-date. This can be a valuable lesson for your participants in how bioinformatic databases can change, or you can run the workshop from the previous archive site instead.

A release on the day of your workshop means both downtime and changes in the data. If we know you’re having a workshop, we’ll make sure that the archive site from the previous release is up and working before we take the main site down, so that you have something to work with, and you can keep using that even once the new site is up.

Need more help?

The Outreach team are here to support you. Just send us an email if you want practical support on how best to run a workshop, if you have any background questions on our data or tools, or indeed with any other questions or problems you might have with Ensembl.