Workshops

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, two or three days. If you are interested in hosting a workshop or want more information, please contact Giulietta Spudich.  Have a look at our free, online browser workshop on the EBI’s train online platform to get a flavour for what it’s like.

For academic institutions our courses are free of charge. However we request that travel, accommodation and subsistence costs of the instructor(s) are reimbursed by the host.

To find out about our current workshop schedule, please see our training calendar or look out for the announcements on our blog.

photos from our workshops

Browser workshop

Our standard 1-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, 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 organization of the Ensembl project
  • Worked example: guided tour of the most important pages of the Ensembl website
  • Data mining with BioMart: retrieving genomic information using a web interface (no programming required).
  • Genebuild: how are Ensembl gene and transcripts predictions made?
  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions
  • Variation: SNPs and other polymorphisms, haplotypes, linkage disquilibrium, structual 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.

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 PC (or Mac) for each participant – 30 is the maximum number of participants
  • Each computer should have a (reasonably fast) internet connection and an internet browser installed (preferably Chrome or FireFox, although Internet Explorer will also work)
  • A computer for the instructor, connected to a projector, with an internet connection and MS PowerPoint installed

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!

Workshop in the Perl APIs

There are 4 Ensembl Perl APIs for which we can provide training: Core, Variation, Comparative Genomics, and Regulation (FuncGen).  The Core API workshop is one day.  Variation, Comparative Genomics, and Regulation can be covered in additional days.

Prerequisite: Knowledge of Perl

If you are already using the Perl APIs, you can post questions on our popular developers’ mailing list.

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.

Send any queries about our workshops, or anything else Ensembl-related to our helpdesk email.