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 Emily Perry. 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. However we request that travel, accommodation and subsistence costs of the instructor(s) are reimbursed by the host. We also request that hosts print workbooks for all of the participants.
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.
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 organisation 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 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.
The only prerequisite for the browser workshop is general knowledge of molecular biology and genomics and a familiarity with web browsers.
- 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
- Booklet printing for all the participants
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.
Workshop in the Perl APIs
There are four 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.
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.
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!
I want to host a workshop – what should I do?
Send any queries about our workshops to Emily Perry.