Ensembl REST API workshop, Cambridge, 11 April 2019


  Thursday 11 April 2019


University of Cambridge - Downing Site,  Cambridge CB2 3AR,  United Kingdom

Application opens: 

Monday 21 January 2019

Application deadline: 

Wednesday 10 April 2019


First come, first served

Registration fee: 

Free for University of Cambridge students

Course Overview

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 scripts to call them.
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


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

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 scripts to access data via the Ensembl REST API


This course will include the following modules:

  • Ensembl and the gene model
  • What is REST
  • Ensembl REST API features
  • Fetching a single endpoint
  • Decoding the response
  • Linking endpoints together
  • POST endpoints
  • Rate limiting