Ensembl REST API workshop (ONLINE TRAINING)

Prerequisites

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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.

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

• 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 registered 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

• 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.

Number of sessions: 1

Bioinformatics, Data retrieval

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

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

Presentations and practicals

• Free for registered 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

1

A number of times per year

• Using the Ensembl Genome Browser (ONLINE LIVE TRAINING)