Workshops and Training
The Ensembl Outreach team regularly organises workshops. We offer two workshops, each of which runs over one day: The new Ensembl Genome Browser workshop, and the Ensembl Train the Trainer workshop.
The new Ensembl
The Ensembl project is transitioning to our new website over 2026 and 2027. We offer a newly designed training programme about the new site and data. The new Ensembl provides fast access to more genome data than ever before. The Ensembl 116 and Ensembl 63 versions will remain available as tools enabled archives so these can be used as they are now for a long time. We will prioritise training on the new Ensembl over the transition period.
If you are interested in hosting a workshop or want more information, please contact our helpdesk. Have a look at our free, on-demand content on EMBL-EBI Training to get a flavour of what it’s like.
For academic institutions our courses are free of charge. We are able to completely cover the costs of workshops held in low-income or middle-income countries (defined by the OECD for the Wellcome Trust), however we request that travel, accommodation and subsistence costs of the instructor(s) are reimbursed by the host in high-income countries. This document lists the full breakdown of the costs involved and the organisation we expect from hosts.
All workshops are held in English and we are based in Cambridge, UK.
To find out about our current workshop schedule, please see our training calendar or send us an email.
Contents
New Ensembl Browser Workshops
Our standard one-day browser workshop offers participants the possibility of gaining lots of hands-on experience in the use of the new Ensembl genome browser, but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers.
Content
The workshop consists of a series of modules, listed below. Most modules consist of a presentation and a demonstration of the tools, followed by the opportunity to do practice using the browser. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl. The exact mix of modules can be varied, depending on the preferences of the participants.
- Introduction to Ensembl: origin, goals and organisation of the Ensembl project
- Genome selection: information about different genome assemblies and Ensembl releases
- Visualising data: access genomic data via the browser, including genetic variants and regulatory elements in Ensembl
- Ensembl annotation: learn about the Ensembl annotation process and its data sources
- Access scales: different scales of accessing Ensembl data (file-based and programmatic access)
- Ensembl tools: explore Ensembl tools to map sequences and interpret variant consequences
A typical one-day workshop will consist of the first four of these modules, plus other modules of your choice. We run a pre-course survey to identify participants’ interests, and customise the course.
Feedback from previous Ensembl courses: “The workshop was an eye-opener to me. It opened my eyes to aspects of bioinformatics I will love to explore. “ Browser workshop, Nigeria, Feb 2022
Learning outcomes
At the end of this course participants should be able to:
- Navigate the new Ensembl interfaces to identify available genomic data
- Examine genome assembly details to select assemblies suitable for your work
- Explore genes, variants and regulatory annotations and their sources
- Outline the various data and tools available for programmatic and file-based access
- Use Ensembl tools such as Ensembl Variant Effect Predictor (VEP) to determine variant consequences
Programme
Times can be adjusted to suit the timetable of the institute:
| Time | Content |
|---|---|
| 09:30-10:15 | Introduction to Ensembl and selecting genomes |
| 10:15-10:45 | Visualising genome data - genes and transcripts |
| 10:45-11:00 | Tea/Coffee Break |
| 11:00-11:30 | Visualising genome data - variation, regulatory elements, related genes |
| 11:30-12:00 | Ensembl Annotation - how genome data is generated and integrated |
| 12:00-12:20 | Access scales - from gene to whole genome |
| 12:20-13:20 | Lunch* |
| 13:20-14:20 | Ensembl Tools - Ensembl Variant Effect Predictor and BLAST* |
| 14:20-14:30 | Wrap Up |
* optional modules depending on the interests of the participants
Prerequisites
This course can be run for a maximum of 30 people. It is aimed at wet-lab scientists and bioinformaticians. Participants should have degree-level understanding of molecular biology/genetics and be proficient at using web browsers.
Requirements
- Computer room with a computer for each participant, computers may be brought laptops as long as power and internet (wi-fi) are available
- Each computer should have a (reasonably fast) internet connection and an up-to-date internet browser installed (preferably Chrome or FireFox)
- A computer for the instructor, connected to a projector, with an internet connection
Tailored courses
We can also run tailored courses that focus on particular aspects of the Ensembl browser or on particular topics. In the past we have held courses that focus on:
- Comprehensive Ensembl Browser
- Ensembl and gene regulation
- Particular Ensembl Genomes taxa (eg Plants, Fungi, Protists, Metazoa or Bacteria)
- Particular Ensembl species
We are open to your ideas – just let us know and we can discuss your requirements.
Because of the specialisation of these courses, it is sometimes necessary to have a second instructor to teach some parts of the course. We may also suggest further pre-requisites and software requirements depending on the topics of interest.
Train the Trainer workshops
The Train the Trainer workshops enable individuals at host institutes to deliver their own Ensembl browser workshops. These are especially beneficial for hosts in low-middle income countries, or where funds are limited to bring over our Ensembl trainers on a regular basis.
Content
The Ensembl Train the Trainer course empowers trainers at institutes around the world to teach their own Ensembl training courses, allowing the knowledge and skills they learn to be passed onto future generations of scientists.
Participants will learn about the general principles of training, along with the specifics of how Ensembl prepare their training courses. The course includes a practical element where participants can practice delivering training and receive feedback on their training style.
Learning outcomes
After this course participants should be able to:
- Describe what makes good/bad training and the skills needed by a trainer
- Appreciate their own learning style, how it may differ to others and how we can deliver training appropriate to different learning styles
- Use existing Ensembl training materials to create their own training materials
- Deliver a short training course on using an aspect of Ensembl
Programme
Times can be adjusted to suit the timetable of the institute:
| Time | Content |
|---|---|
| 09:30-10:30 | Overview of what is involved in training |
| 10:30-10:50 | Tea/Coffee Break |
| 10:50-12:00 | Training styles |
| 12:00-12:30 | Structure of Ensembl training |
| 12:30-13:30 | Lunch Break |
| 13:30-15:00 | Preparation for practical |
| 15:00-15:20 | Tea/Coffee Break |
| 15:20-17:30 | Delivery of practical training sessions and group feedback |
Participants
This course can be run for a maximum of six people. Participants must be enthusiastic and willing to deliver training in future. Participants must have attended the Ensembl Browser course.
If Ensembl are delivering a number of browser courses in different institutes in a city or area, we may suggest holding a single Train the Trainer course in that city, and invite a fixed number of participants from each host institute. In that case, we would ask one host to host the course for all.
Requirements
For these course we require a meeting room with sufficient space for the trainer and trainees, and a projector for the trainer. Trainees will need computers for preparing their practice training sessions, which can be brought laptops, or they can disperse to shared computers.
Virtual Training
All our courses can be be held online, but special considerations will be needed for the Train the Trainer which the Ensembl team will raise in early discussions.
We can set up virtual classrooms with your institute, holding live interactive webinars with our trainers. These can be held as one single long event, or a number of short sessions over days or weeks, timed to match your timezone. The advantage of hosting a training workshop for your institute is that we can tailor the course to the needs of the institute and trainees.
We are running regular open public courses, which anyone can register for. Registration links and further information for upcoming open courses can be found on the Ensembl blog. These are useful if you are interested in training but your colleagues aren’t, but they may be at inconvenient times of day for your timezone, and will not be so tailored for your needs.
Geek for a week
For a more immersive experience, the “Geek for a Week” scheme allows developers and researchers to work alongside Ensembl team members for a short intensive collaborative project.
General Information
Course charges
Ensembl staff are supported by our scientific funders to produce workshop materials and to deliver workshops. Because of this, the project does not charge for these services to academic hosts, although there are fees for commercial hosts.
In a high-income countries, we ask our hosts to pay the expenses, including the travel, accommodation and subsistence of the trainer. If we are delivering workshops in low-income or middle-income countries (defined by the OECD for the Wellcome Trust), these expenses will be covered by us.
We understand that there are costs involved in hosting a workshop and some hosts may charge a minimal fee to participants in order to recover these costs. Ensembl aims to get training out to as many people as possible, therefore we prioritise workshops where no cost is incurred by attendees.
Should you have any further questions about this please contact our helpdesk.
Certificates on request from host
Only on request from the host, participants can opt to receive an e-certificate of attendance for all our courses. This e-certificate of attendance does not confer any qualification or license to the recipient, it simply states that they attended the course.
