Courses and other events

Fri, OCTOBER 26th, 2018

09:00-17:00

Ensembl browser workshop

Location: University of Turku, Natura building, IT class 420
Lecturer: Dr Astrid Gall, Ensembl Outreach Officer, European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI)
Organiser: EMBL-EBI, CompLifeSci research programme and Biocity Turku

The Ensembl project (www.ensembl.org) provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-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 (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 of our browser as well as frequent users.

Programme
The workshop consists of a series of modules, listed below. All modules include a presentation and a demonstration of the tools, followed by exercises. Participants are encouraged to bring problems/questions about their research, and we will try to tackle these during the workshop.

  • Introduction to Ensembl: origin, goals and organisation of the Ensembl project
  • 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, the Variant Effect
  • Predictor (VEP) tool
  • Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data
  • Data export with BioMart: retrieving genomic information using a web interface (no programming required).

The workshop consists of the first three modules, plus two other modules. The two additional modules depend on what participants express an interest in when they register.

Prerequisites
The only prerequisite is a general knowledge of molecular biology and genomics and a familiarity with web browsers.

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

Learning outcomes
Participants should be able to:

  • view genomic regions and manipulate the view to add features they are interested in
  • explore information about genes, their sequences and other 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.

For more information, please contact miina.nurmi@utu.fi