Ensembl REST API workshop, American University in Cairo, 22nd January 2020

Date:

  Wednesday 22 January 2020

Venue: 

American University in Cairo - AUC Avenue, Cairo,  11835, Egypt

Application opens: 

Monday 14 October 2019

Application deadline: 

Saturday 02 November 2019

Participation: 

Open application with selection

Registration fee: 

Free

Registration closed

Find other similar courses »

Course Overview

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. Our sister project Ensembl Genomes covers bacteria, plants, fungi, protists and (invertebrate) metazoa. This workshop is aimed at researchers and developers interested in exploring the data beyond the websites. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/R/Perl scripts to call them.

This course does not cover the background to the Ensembl data and participants should have previously attended an Ensembl browser course (such as the one on the 15th October). This course does not cover the basics of programming.


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.

Audience

Bioinformaticians and wet-lab biologists who can program in Perl, Python or R. The Ensembl browser workshop is a pre-requisite for this course.

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/Perl scripts to access data via the Ensembl REST API

Programme

09:30-10:00    Overview of the Ensembl REST API
10:00-11:00    Accessing GET queries with the Ensembl REST API
11:00-11:20    Tea/Coffee Break    
11:20-12:30    Decoding json and chaining REST queries together
12:30-13.15    Lunch
13:15-14:30    Accessing POST queries with the Ensembl REST API
14:30-15:00    Rate limiting