Ensembl REST API workshop (ONLINE LIVE TRAINING)

Prerequisites

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.

• 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, including for University of Cambridge students. 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.

• 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

• 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 Google account as the training will utilise Jupyter Notebooks hosted by Google Colab. A free account can be created here.

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

All times are approximate. End time extended to accommodate timetable.

Tea/Coffee Breaks around 11am and 3pm

• 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

1

A number of times per year

• Using the Ensembl Genome Browser (ONLINE LIVE TRAINING)