Workshops and Training
The Ensembl Outreach team regularly organises workshops. Genome browser workshops (see below for more information) are usually one day; workshops on the use of the Ensembl REST Application Programming Interfaces (APIs) are one day. If you are interested in hosting a workshop or want more information, please contact our helpdesk. Have a look at our free, online browser workshop on the EBI’s train online platform 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.
Training during the COVID-19 pandemic
We are still delivering training during the COVID-19 pandemic. Instead of training in person, we have shifted our efforts to online training. Both the Browser and the REST courses listed below can be held online.
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.
Contents
- Browser Workshops
- REST API Workshops
- Train the Trainer Workshops
- Geek for a week
- General Information
Browser Workshops
Our standard one-day browser workshop offers participants the possibility of gaining lots of hands-on experience in the use of the 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 exercises. 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
- Genebuild: how are Ensembl gene and transcripts predictions made?
- Data export with BioMart: retrieving genomic information using a web interface (no programming required).
- Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
- Variation: SNPs and other polymorphisms, haplotypes, linkage disequilibrium, structural variants like CNVs
- Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data
A typical one-day workshop will consist of the first three of these modules, plus two other modules of your choice. We run a pre-course survey to identify participants’ interests, and customise the course.
Feedback from previous courses: “There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become” Browser workshop, CRUK, April 2016
“Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert.” Browser workshop, Cardiff, March 2014
Participants can opt to receive an e-certificate of attendance for this course. This e-certificate of attendance does not confer any qualification or license to the recipient, it simply states that they attended the course.
Learning outcomes
At the end of this course participants should be able to:
- view genomic regions and manipulate the view to add features they are interested in.
- explore information about genes and their sequences, and gene data in bulk using BioMart.
- analyse genomic variants and associated phenotypes and their own variation data using the VEP.
- view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.
Programme
Times can be adjusted to suit the timetable of the institute:
| Time | Content |
|---|---|
| 09:30-10:30 | Introduction to Ensembl and the Region in Detail View |
| 10:30-10:50 | Tea/Coffee Break |
| 10:50-12:00 | Genes and transcript annotation |
| 12:00-13:00 | Lunch Break |
| 13:00-14:30 | Variation data and the VEP* |
| 14:30-14:50 | Tea/Coffee Break |
| 14:50-15:30 | Regulatory data* |
| 15:30-16:10 | Comparative Genomics* |
| 16:10-17:15 | BioMart |
| 17:15-17:30 | 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
- 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
- Booklet printing for all the participants
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 the 1000 genomes project
- Ensembl and gene regulation, including data from ENCODE, Blueprint, RoadMap epigenomics and more
- 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.
REST API Workshops
The Ensembl REST API allows language agnostic programmatic access to Ensembl data. Our half-day workshop offers an introduction the REST API and its documentation, and how to access our data.
Content
The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.
Feedback from previous courses: “Wish I had taken the course long time ago. Didn’t know before how good and powerful APIs are!” API workshop, EMBL-EBI, January 2016
“I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset.” API workshop, Cambridge, December 2013
Participants can opt to receive an e-certificate of attendance for this course. This e-certificate of attendance does not confer any qualification or license to the recipient, it simply states that they attended the course.
Learning outcomes
After this course participants should be able to:
- Synthesise the data types accessible through the Ensembl REST API
- Understand the methods in the Ensembl REST API
- Navigate the Ensembl REST API documentation to find available methods
- Write scripts to access data via the Ensembl REST API
Programme
Times can be adjusted to suit the timetable of the institute:
| Time | Content |
|---|---|
| 09:30-10:00 | Overview of the Ensembl REST API |
| 10:00-10:30 | Accessing GET queries with the Ensembl REST API |
| 10:30-10:50 | Tea/Coffee Break |
| 10:50-13:00 | Decoding json and chaining REST queries together |
| 13:00-14:00 | Lunch |
| 14:00-15:00 | Accessing POST queries with the Ensembl REST API |
| 15:00-15:30 | Rate-limiting |
Prerequisites
This course can be run for a maximum of 15 people. Participants must be able to code in Python, Perl or R. Participants should be familiar with the data in Ensembl and we recommend they attend the browser course. The training will utilise notebooks hosted by Google Colab.
Requirements
For these courses we require a Computer room with a computer for each participant. The computers should be equipped with:
- 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
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.
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
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.
