Ensembl REST API course – 27th-28th November 2017

Date:

 Monday 27 Tuesday 28 November 2017

Venue: 

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

Application opens: 

Wednesday June 28 2017

Application deadline: 

Friday November 24 2017

Participation: 

First come, first served

Contact: 

Emily Perry

Registration fee: 

free

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 the core, compara, variation and functional genomics (regulation) databases and the REST API.
http://www.ensembl.org/info/docs/api/index.html

For each of these  the most important objects and their methods will be presented. This will be followed by practical sessions in which the participants can put theoretical learning into practice by writing their own scripts in their preferred language.

Note: Some programming is a prerequisite for the course.

Beginner and regular users of the Ensembl REST API are welcome.

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 any language.

Syllabus, tools and resources

During this course you will learn about:
  • Introduction to Ensembl: Data models, features
  • APIs in Ensembl: Perl and REST, navigate documentation
  • Overview of REST and Functional groupings.
  • Accessing genomic regions (slices), genes, transcripts, translations and repeats.
  • Accessing genomic variants, their alleles and allele frequencies, genotypes, phenotypes, linkage disequilibrium and genes they hit.
  • Accessing gene trees, homologues and families.
  • Accessing Regulatory Features, identifying variants within features.

Outcomes

After this course you should be able to:

  • Describe the data types accessible through the Ensembl REST API
  • Indicate the methods in the Ensembl REST API
  • Navigate the Ensembl REST API documentation to find available methods
  • Use the Ensembl REST API to access data

Programme

The course will run 9.30am-5pm on both days, with a tea/coffee break mid-morning and mid-afternoon, and a lunch break each day.

 

Time Topic Instructor
Monday morning Core: the basics of using the REST API and accessing gene and region data Kieron Taylor
Monday afternoon Variation: fetching variant information, including consequences, phenotypes and frequencies Helen Schuilenburg
Tuesday morning Regulation: finding features that regulate gene expression Thomas Juettemann
Tuesday afternoon Compara: finding homolgoues and alignments Carla Cummins