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Thu 11 Apr 2019
09:30 - 15:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Ensembl REST API workshop
Prerequisites

Thu 11 Apr 2019

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 how to use the Ensembl REST APIs, including understanding the major endpoints and how to write scripts to call them.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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
  • Participants must be able to code in Python, Perl or R.
  • Participants should be familiar with the data in Ensembl and we recommend they attend the Ensembl browser course.
  • Each participant must have a free Microsoft account as the training will utilise Jupyter Notebooks hosted by Microsoft Azure. A free account can be created here.
Sessions

Number of sessions: 1

# Date Time Venue Trainer
1 Thu 11 Apr   09:30 - 15:30 09:30 - 15:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Astrid Gall
Topics covered

Bioinformatics, Data retrieval

Objectives

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 scripts to access data via the Ensembl REST API
Aims

This course aims to provide an overview of the Ensembl REST API.

Format

Presentations and practicals

Timetable

Time Topics
9:30 – 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 – 13:00 Decoding json and chaining REST queries together
13:00 – 14:00 Lunch (not provided)
14:00 – 15:00 Accessing POST queries with the Ensembl REST API
15:00 – 15:30 Rate-limiting
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) 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

1 day

Frequency

A number of times per year

Related courses
Theme
Specialized Training

Booking / availability