Ensembl REST API course, July 2018

Date:

  Thursday 12 July 2018

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 14 May 2018

Application deadline: 

Thursday 05 July 2018

Participation: 

First come, first served

Contact: 

Emily Perry

Registration fee: 

free

Registration closed

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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

Audience

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

Syllabus, tools and resources

During this course you will learn about:

  • Introduction to Ensembl: Data models, features
  • APIs in Ensembl: Perl and REST, navigating documentation
  • Running single REST endpoints
  • Using Python scripts to access GET and POST endpoints with the Ensembl REST APIs

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

Programme

09:30-10:00    Overview of the Ensembl REST API
10:00-10:30    Accessing GET queries with the Ensembl REST API
10:30-10:50    Tea/Coffee Break    
10:50-12:00    Decoding json with Python and chaining REST queries together
12:00-13:00    Accessing POST queries with the Ensembl REST API