You might know that we offer training courses on using the Ensembl browser, but did you know that we also offer Ensembl REST API and Ensembl Train the Trainer courses? We can come to you to deliver any of these courses at your institute and we don’t charge any fees. If you’re in a low-middle income country, we don’t even charge you for expenses.

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Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl.

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One of the biggest headaches when working with insertions and deletions is how many different ways you can represent the same variant. If you’re looking to find out if there’s already known allele frequencies or phenotypes at a locus, you want to make sure that you find the right one. The VEP can take that headache away through normalisation of variants.

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Some Variant Effect Predictor (VEP) jobs are small, just ten or fewer variants, and that’s easy. Some VEP jobs are big, if you do variant calling on one whole human genome, that’s five million variants! The more variants you have, the more computing power the VEP needs to process them, which can make it slow. But there are ways to speed it up.

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We think conferences are great opportunities to use talks and posters to tell people about all the cool stuff we’re developing, provide training with workshops and learn more about what’s going on in our fields of interest. Ensembl team members attend many conferences a year and 2018 is no exception, we’re planning to attend twenty (so far)!

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We’re holding an Ensembl Perl API course at the Genome Campus in the UK in April. The course give you chance to learn how to access the database directly from the people who produce the databases and write the APIs themselves. It is aimed at bioinformaticians and wet-lab scientists who are familiar with Object Oriented Perl.

This four-day course costs only £140, which includes daily transport to the campus from Cambridge city centre and refreshments (the fee is to cover only these expenses).

Please visit the course page for more details on the content and how to apply.

Following the success of last year’s course, we’re pleased to announce a second Free Ensembl Webinar Course.

This course allows you to learn about Ensembl for free from the comfort of your own office (or bed, no-one’s judging you), with the ability to interact live with the instructors. Perfect for those who can’t attend or host one of our live courses.

What is it?

The Ensembl online training series comprises a series of live webinars, once a week over seven weeks. Each webinar explores a specific aspect of Ensembl data or tools with a presentation and a demonstration – see the online course for details. You can then practice what you’ve learnt over the following week with online exercises.

Not all of the topics will be useful to you, so you can dip in and out of the webinars. If life gets in the way and you miss one you are keen on, we will post the videos to our YouTube channel and YouKu for those of you in China and embed them in the online course so that you can catch up.

What makes it special is that the course is fully interactive. If you attend the live webinars, you will have an opportunity to ask the instructors questions in real time. Afterwards, while you work on the exercises, you can interact with the instructors and other participants via our dedicated Facebook group. If you prefer not to use Facebook, you can also email us for help. Plus, you’ll be able to re-watch all or part of the videos at your leisure.

When is it?

We start on the 6th April, and will hold seven webinars on Thursday mornings, up until the 18th May. The live webinars will take place at 9 am BST (GMT+1), but if you are unable to attend live, the videos will be posted shortly afterwards. Since last year’s course was held in the afternoons, good for our American friends, we’re hoping that this morning course will be easier to access for anyone in Asia or Oceania.

After the live course finishes, we will leave the full course of recordings and exercises online, so that you can take it independently whenever you choose.

69.7% are very likely to recommend this course, 30.3% are likely to.

Is it any good?

We think so, but don’t take our word for it. Here’s what the attendees from last year had to say:

“Thank you. I really appreciate having access to this course. I’ve learned a lot.”

“Thank you so much for organising this. I really enjoyed!”

“Thank you; the course is very useful. I´m very happy”

How do I sign up?

You can visit the course pages to see what’s going on without signing up. If you want to attend the webinars live, you will need to sign up (or sign up here from China), but there’s no charge for doing so. You may also wish to join the Facebook group.

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.