Ensembl Browser workshop, Rotterdam, The Netherlands, 13-14 February 2018


 Tuesday 13 Wednesday 14 February 2018


Erasmus MC Rotterdam - Erasmus MC, 's-Gravendijkwal 230, 3015 CE,  Rotterdam, Netherlands

Application opens: 

Monday 08 January 2018

Application deadline: 

Monday 12 February 2018


First come, first served

Registration fee: 

€ 300,- Free of charge (100 % discount) for members of MolMed.

Registration closed

Find other similar courses »

Course Overview

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 2-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.

The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users. 

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

If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.


Wet-lab researchers and bioinformaticians

Learning outcomes

Participants should be able to:

  • view genomic regions and manipulate the view to add features you are interested in.

  • explore information about genes and their sequences, and gene data in bulk using BioMart.

  • analyse genomic variants and associated phenotypes and your 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.


Tuesday 13th February

  • Introduction to Ensembl: Origin, aims and organisation of the Ensembl project

  • Genes and Transcripts: How are Ensembl gene and transcripts predictions made?

  • Variation: SNPs and other polymorphisms, structural variants such as CNVs, phenotypes, haplotypes, linkage disequilibrium

  • The Variant Effect Predictor (VEP): Prediction of functional consequences of known and unknown variants

Wednesday 14th February

  • Comparative genomics: Homologues, gene trees, whole genome alignments, protein families, synteny; OR Regulation: Features involved in gene regulation, integration of ENCODE, Roadmap Epigenomics and Blueprint data

  • BioMart: Data-mining and export of custom dataset using the web interface (no programming required)

  • Ensembl Tools & Advanced Access: E.g. BLAST/BLAT, converting files/assemblies/identifiers, upload and visualization of custom data, accessing large data sets via FTP

  • Summary, Q & A, and how to get further help

The course will be tailored to the interests that participants express when they register.