Ensembl TrainingEnsembl Home

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 Application Programming Interfaces (APIs) can be one to four days. 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.

To find out about our current workshop schedule, please see our training calendar or send us an email.

Request a workshop

Contents

  1. Browser Workshops
  2. REST API Workshops
  3. Perl API Workshops
  4. 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.

Prerequisites

The only prerequisite for the browser workshop is general knowledge of molecular biology and genomics and a familiarity with web browsers.

Requirements

  • Computer room with a computer for each participant – 30 is the maximum number of participants
  • 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. We can offer a half-day or two-day workshop, offering an introduction the REST API and its documentation, and how to access gene data, or exploring all data types in Ensembl through REST, respectively.

Content

There are four available modules, each half a day long, which provide outlines, exercises and solutions to programmatic problems. These focus on particular data types and can be selected depending on the interests of the participants:

  • Genes, Transcripts, Proteins, cross references, GO annotations(this module forms the one-day course and is a requirement for any course).
  • Whole genome alignments, gene trees, homology
  • SNVs, complex indels, somatic variation
  • Functional annotation including promoters, enhancers, CTCF binding sites and arrays

Prerequisites

Attendees should be familiar with the Unix command line and have a working knowledge of a programming language. We are able to provide extensive support for Perl and Python programmers, but our support for other programming languages may be limited.

Requirements

For these courses we require a Computer room with a computer for each participant – 20 is the maximum number of participants. The computers should be equipped with:

  • A (reasonably fast) internet connection and an up-to-date internet browser installed (preferably Chrome or FireFox)
  • Perl 5.14.2 or later and Python3 installed with HTTP libraries
  • A computer for the instructor, connected to a projector, with an internet connection

Perl API Workshops

Our Perl API workshops describe how to access Ensembl through our Perl APIs. The Perl APIs offer a greater breadth of data than the REST APIs. We can offer a one day workshop that introduces the APIs and their documentation, and how to access gene data, or a longer four day course exploring the different sections of the APIs in detail.

Content

The workshop consists of a number of modules providing outlines, exercises and solutions to programmatic problems. There are four available modules, each one day long, which can be selected depending on the interests of the participants, which teach them how to access:

  • Genes, Transcripts, Proteins, cross references, GO annotations via the Perl Core API (this module forms the one-day course and is a requirement for any course).
  • Whole genome alignments, gene trees, homology via the Perl Compara API
  • SNVs, complex indels, somatic variation via the Perl Variation API
  • Functional annotation including promoters, enhancers, CTCF binding sites and arrays via the Perl Regulation API

Prerequisites

Attendees should be familiar with the Unix command line and have a basic working knowledge of Object Oriented Perl.

Requirements

For these courses we require a Computer room with a computer for each participant – 20 is the maximum number of participants. The computers should be equipped with:

  • A (reasonably fast) internet connection and an up-to-date internet browser installed (preferably Chrome or FireFox)
  • Perl 5.14.2 or later
  • The Ensembl APIs and dependencies installed (we can provide a VM for this)
  • A computer for the instructor, connected to a projector, with an internet connection

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

We don’t usually make and give out certificates of attendance to participants, however if the host wishes to do this, this is fine by us and we will be happy to sign them.