Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments.

Who is this course for?

Bioinformaticians and wet-lab biologists who can program in Python or R.

What will I learn?

Learning outcomes

After this course participants should 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 Python/R scripts to access data via the Ensembl REST API

Course content

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/Perl/R scripts to call them.

During this course you will learn about:

• Introduction to Ensembl: Data models, features
• The Ensembl REST API, navigate documentation
• Overview of REST and functional groupings
• Accessing genomic regions (slices), genes, transcripts and translations
• Accessing genomic variants, their alleles and allele frequencies, genotypes and phenotypes
• Accessing gene trees and homologues
• Accessing regulatory features

Feedback from previous courses:

"Wish I had taken the course long time ago. Didn't know before how good and powerful APIs are!" API workshop, EMBL-EBI, January 2016

"I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset." API workshop, Cambridge, December 2013

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

Trainers

Attendance at this workshop is allocated on a first come, first served basis. Please complete the online application form to register.