Ensembl browser and REST API course, Yeditepe University

Date:

 Thursday 31 January Friday 1 February 2019

Venue: 

Yeditepe University - Istanbul,  34755,  Atasehir,  Turkey

Participation: 

By invitation

Contact: 

Emily Perry

Registration fee: 

free

Course Overview

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 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. This is followed by an optional day to look at directly accessing the Ensembl database using the REST APIs.

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.

Audience

Bioinformaticians who can code in Python, Perl or R.

Learning outcomes

After the browser course, participants should be able to:

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

  • explore information about genes and their sequences, and gene 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.

After the optional REST API course, participants should also be able to:

  • Synthesise the data types accessible through the Ensembl REST API
  • Understand the methods in the Ensembl REST API
  • Navigate the Ensembl REST API documentation to find available methods
  • Write scripts to access data via the Ensembl REST API