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Instructor-led course

Provided by: Bioinformatics


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Ensembl REST API workshop
Prerequisites


Description

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 using the REST API to query the core, variation, compara and functional genomics (regulation) databases.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • Bioinformaticians and wet-lab biologists who can program
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
  • Further details regarding eligibility criteria are available here
Prerequisites
  • Some basic programming experience is a prerequisite for the course. The REST API works for any language, but in the workshop we can only offer assistance to PERL and Python programmers
  • Beginner and regular users of the Ensembl API are welcome
Topics covered

Bioinformatics, Data retrieval

Objectives

After this course you should be able to:

  • Understand the data types accessible through the Ensembl REST API
  • Understand the methods in the Ensembl REST API
  • Practice using the Ensembl REST API to access data
Aims

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.
Format

Presentations and practicals

Timetable

Day 1 Topics Speaker(s)
9:30 – 12:30 Introduction to the REST API and working with genes, transcripts and genomic regions Matt Laird
12:30 - 13:30 Lunch
13:30 – 17:30 Accessing genomic features that regulate gene expression Thomas Juettemann
Day 2
9:30 – 12:30 Identifying and exploring genetic variation data

Anja Thormann
12:30 - 13:30 Lunch
13:30 – 17:30 Exploring gene trees and homologues

Wasiu Akanni
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2 days

Frequency

A number of times per year

Related courses
Theme
Specialized Training

Events available