A guide to hosting an Ensembl Workshop

Are you interested in having us come to your institute to deliver an Ensembl workshop, but are not quite sure what it involves? This blog is a guide for you.

What workshops does Ensembl offer?

We offer three types of workshops, which are summarised here (full details in the header links):

  1. Browser workshop (full day, 09:30-17:30)
    • This course leads participants through the theory and origin of the data we host in Ensembl, and how to use the websites (www.ensembl.org and www.ensemblgenomes.org) to access this data.
    • There are no prerequisite requirements for this workshop.
  2. REST API workshop (partial day, 09:30-15:30)
    • This workshop builds on what was learnt in the browser workshop, and shows people how to access Ensembl data programmatically through our REST API server.
    • We teach this course using Jupyter notebooks and participants will need to have a (free) Microsoft account to access these. The notebooks we have available are in Perl, Python and R.
    • Attending the Ensembl Browser workshop is a prerequisite for this course, and it is essential that participants know how to code in either Perl, Python or R.
  3. Train the Trainer workshop (full day, 09:30-17:30)
    • This is a workshop that we are currently only offering to host institutes in low-middle Income countries, as part of the grant that we were awarded.
    • This workshop trains participants to be able to deliver their own Ensembl workshops, focusing on adult teaching theory (andragogy) and developing practical training materials.
    • Attending the Ensembl Browser workshop is a prerequisite for this course.


The stages in hosting an Ensembl workshop

Figure 1: Key stages involved in hosting an Ensembl workshop

Stage 1: Get in touch

The first thing to do is email us [LINK] to express your interest in having a workshop delivered at your institute. We are commonly booked quite far in advance, so the earlier you can email us the better, especially if you have a specific (inflexible) date in mind. Key things to include in this initial email are:

  • Which workshop(s) you would like.
  • Who the target audience is (i.e. education level, species of interest).
  • Preferred dates.
  • A specific location (i.e. which institute, rather than a city location), or locations.

We will then respond and agree or negotiate a date that we can accommodate the workshop(s).

Stage 2: Agree to the host expectations

This is a dull but necessary step; we need to know that you are committed to hosting us, and you need to know that we are committed to come to you! We will send you this document for you to review and state that you agree with the expectations outlined within it. Things covered include expenses repayments and minimal number of participants registered amongst other things.

A key question is ‘how much does an Ensembl workshop cost to run?‘, well this varies greatly depending on your location. We do not charge speaker fees for non-profit organisations but if your institute is in a high income country then we will ask you to cover the expenses of the trainer, including travel, accommodation and subsistence for the duration of the trip. To reduce these costs we are happy to deliver workshops at multiple institutes in the area, so you can contact neighbouring institutes to see if they are interested in offering an Ensembl course, and can split the costs with you. If you need to keep the costs to a budget then you are welcome to agree a realistic budget with us at this point.


Figure 2: Map of low-middle income countries, according to the OECD

If you are inviting us to come to your institute in a low-middle income country (as defined by the OECD, Figure 2), then we will not require you to cover the trainers expenses, but please be aware that we cannot cover the costs associated with the running of the course, such as room booking fees or catering. More about our low-middle income countries grant from the Wellcome Trust.

Stage 3: Meeting your trainer

There are four members of the Ensembl Outreach team. Once dates have been booked in by Emily, our team leader, we will assign a trainer to deliver the workshop. It is usually based on availability, sometimes expertise, and if more than one person is available we get to express our preference (i.e. call ‘dibs’) for workshops in places we’re excited to go to! Once decided, you’ll be in contact directly with the trainer on the practical aspects of delivering the course. 

Stage 4: Practical arrangements

  • Reimbursements.

If you are in a high-income country, then you will be required to cover the trainer’s expenses as described in Stage 2. The trainer will contact you to see if you would like your institute to book the accommodation and travel directly, or whether you would like the trainer to manage the bookings and ask for reimbursement from your institute after the workshop is completed. Most prefer to do the latter option, as the trainer will need to submit expenses for subsistence (food and drink) and domestic travel (public transport or taxis) after the workshop regardless.

  • Accommodation.

The trainer will usually ask for recommendations on accommodation, as you know the area best and institutes often have existing relationships with accommodation providers close to Universities and Companies. Safety and proximity to the institute are the most important factors to us.

  • Travel

We will also commonly ask if you have any recommendations for international or domestic travel, particularly if there are multiple airports or concerns about the safety or ease of payment for local travel.

  • Room bookings

It is the host’s responsibility to find and book a suitable room for the course. The full requirements are listed in the hosting expectations document.

  • Breaks

For a full day course we have two 30 minute coffee breaks, and an hour lunch break incorporated into the programme. It is not necessary for you to arrange catering for the participants or the trainer delivering the workshop, but many institutes choose to do so. 


Step 5: Course registration and pre-course surveys

  • Registration

We require a minimum of 10 participants to be registered for us to travel and deliver a course, as you will have agreed to in the hosting expectations document. We need to make sure that our time is well spent, as days out of the office mean that we are unable to carry out other work. It is the responsibility of the host to arrange registration for the course.

With your permission we will also create an event on the EBI training pages (for example this one from Ben’s workshop in Lagos, Nigeria) which will give you extra publicity for the workshop, and is useful to us to demonstrate how far-reaching our training is.

  • Pre-course survey

We will send you a pre-course survey for you to circulate to participants registered for the course. This survey lets us know what topics are of interest to the participants and what their species of interest is so we can tailor the course appropriately; there’s no point in us teaching human data resources if everyone is studying plants!

Some organisers incorporate this into the registration process, while others choose to circulate to the participants once registered. It is essential that we have the responses to the pre-course survey two weeks before the course is due to be delivered so that we can tailor the materials appropriately.

Figure 3: An example of responses to a question in our pre-course survey


Step 6: Training materials

Once we have created the materials, we will upload them to the Ensembl training site, where they will be publicly available before and indefinitely after the course. You can find all of the training materials for our past courses here. We will share the materials with you directly, and it is up to you whether you choose to offer printed materials to the participants. We will not print and bring materials for you, and we cannot offer funds to cover the cost of printing.

Step 7: Workshop delivery and feedback

We will exchange telephone numbers with you before we travel and ask that you (or a colleague) meet us at the institute at an agreed location and time, usually 30 minutes before the scheduled start of the workshop so that we can get everything set up and ready.

We will create a course feedback survey and ask course participants to fill this in. This questionnaire will ask participants how they found the different aspects of the course, to help us improve our courses in the future. We will share the results of this survey with you for your records.

Figure 4: An example of the responses to a question on the feedback survey


Once the course is completed and we’re back in the office in the UK we will submit the expenses forms and send you an email with the feedback survey results, and any follow up questions or comments.

What about your new website Ensembl 2020, should I bother hosting a workshop now if everything is about to change?

Yes, we do have a new website coming (more about that here) but it is absolutely still relevant to have an Ensembl workshop before the new website. Much of what is covered in an Ensembl workshop is the theory of the data, and how to interpret it, which will of course still be relevant in the context of the new website. From January 2020 when the first live instances of the website are available we will introduce novel browsing methods in our workshops so that participants have a glimpse of what using Ensembl in the future will be like.