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Instructor-led course

Provided by: Bioinformatics


This course has 1 scheduled run. To book a place, please choose your preferred date:


Fri 24 Jan 2025


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Events available

Ensembl REST API workshop (ONLINE LIVE TRAINING)
Prerequisites


Description

The Ensembl project provides an interface and an infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data, covering over 300 vertebrate species.

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.


If you do not have a University of Cambridge Raven account please book or register your interest here.

Additional information
  • Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
  • Attendance will be taken on all courses and a charge is applied for non-attendance. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
  • Further details regarding eligibility criteria are available here.
Target audience
  • Bioinformaticians and wet-lab biologists who can program
  • Please review the relevant policies.
Prerequisites
  • Participants must be able to code in Python 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 Google account as the training will utilise Jupyter Notebooks hosted by Google Colab. A free account can be created here.
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

System requirements

Participants must have their own computers to work on and a stable internet connection for the duration of the course.

Timetable

Tea/Coffee Breaks around 11am and 3pm

Time Topics
Session 1 Introduction to the Ensembl REST API
Session 2 Accessing GET queries via a browser
Session 3 Scripting around REST API calls
Session 4 Decoding JSON responses
Session 5 Using results: fetching specific data points
12:30 Lunch break
Session 6 Other content types
Session 7 Chaining REST API queries
Session 8 Accessing POST queries: bulk REST API calls
Session 9 Rate-limits
Session 10 Closing remarks
Registration Fees
  • Free for registered University of Cambridge students
  • £ 60/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.
  • £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 120/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

1

Frequency

Once per year

Related courses
Theme
Specialised Research Topics

Events available