Ensembl programmatic access with Perl, April 2018


 Monday 23 Thursday 26 April 2018


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

Application opens: 

Friday 15 December 2017

Application deadline: 

Monday 16 April 2018


First come, first served


Emily Perry

Registration fee: 


Registration closed

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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 APIs.

For each of these the database schema and the API design as well as 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 Perl scripts.

Note: Some basic object-oriented Perl experience is a prerequisite for the course.

Beginner and regular users of the Ensembl 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

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


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

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.


After this course you should be able to:

  • Understand the data types accessible through the Ensembl Perl API
  • Understand the methods in the Ensembl Perl API
  • Navigate the Ensembl Perl API documentation to find available methods
  • Practice using the Ensembl Perl API to access data


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


Time Topic Instructor
Monday Core: the basics of using the Perl API and accessing gene and region data Kieron Taylor
Tuesday Variation: fetching variant information, including consequences, phenotypes and frequencies Anja Thormann and Andrew Parton
Wednesday Regulation: finding features that regulate gene expression Michael Nuhn
Thursday Compara: finding homolgoues and alignments Wasiu Akanni