[All] Fwd: Ensembl Plants Browser and REST API workshop registration

Cath Brooksbank cath at ebi.ac.uk
Thu Oct 14 09:59:18 BST 2021

Dear all - I’d like to alert you to two upcoming plant genomes courses that the Ensembl team will be running at the beginning of November - one on browser-based access, the other on API-based access. I advise early registration as places are limited.



We’re hosting open virtual courses focusing on plant genomes and dedicated to the plant science community. Both workshops will be held between Tuesday – Thursday, with the Browser on 2nd-4th November and the REST API on 9th-11th November 2021 (2pm-5pm GMT). Read on for more information and registration instructions.

The Ensembl Plants Browser workshop

The Ensembl Plants Browser workshop is an introductory workshop aimed at wet-lab scientists and bioinformaticians working with plants, who are new to using Ensembl Plants. This workshop is also suitable for scientists who are familiar with Ensembl Plants, but would like to refresh their knowledge and learn more about Ensembl Plants. The workshop will cover accessing data using the Ensembl Plants genome browser web-interface.

By the end of the course you will be able to:

Navigate Ensembl Plants using the web browser platform
Access main data types in Ensembl Plants: genomes, genes, genetic variation and comparative genomics
Annotate your own variant data with the Variant Effect Predictor (VEP)
Mine Ensembl Plants data using BioMart
Visualise your own data in the Ensembl Plants genome browser

Tuesday 2nd November 2021, 2pm-5pm (GMT)

Introduction to Ensembl Plants.
Ensembl Plants Genes and Transcripts.

Wednesday 3rd November 2021, 2pm-5pm (GMT)

Ensembl Plants Variation and the Variant Effect Predictor (VEP).
Comparative genomics in Ensembl Plants.

Thursday 4th November 2021, 2pm-5pm (GMT)

Custom export of Ensembl Plants data with BioMart.
Visualising your own data in the Ensembl Plants browser.

The Ensembl Plants REST API workshop

The Ensembl Plants REST API workshop is aimed at researchers and developers working with plant genomes and interested in exploring Ensembl Plants beyond the website. The workshop covers how to work with the Ensembl REST APIs using plant examples, including understanding the major endpoints and how to write Python/R scripts to call them. It is important to note that this course will not introduce you to the Ensembl Plants browser and data types or provide an introduction to programming in Python or R. Proficiency in Python or R and attendance at an Ensembl Plants browser workshop are required to register for the REST API course.

By the end of this course you will 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 Python/R scripts to access data via the Ensembl REST API

Tuesday 9th November 2021, 2pm-4:30pm (GMT)

Overview of the REST API and how to query the REST API with URLs. Fetching REST endpoints programmatically.

Wednesday 10th November 2021, 2pm-4:30pm (GMT)

Fetching specific data points from REST queries and other data types.

Thursday 11th November 2021, 2pm-4:30pm (GMT)

Linking REST queries together. Bulk REST API queries with POST and rate limiting.

How do the courses work?

The workshops will be held using the Zoom platform. The Zoom link and further information will be sent to you upon registration. 

On each day there will be two lectures plus interactive exercise sessions, with a short break in between.

You will be able to ask questions of the instructors during the lectures and discuss with both the instructors and the rest of the participants during the exercises.


You can register for either (or both) the Ensembl Plants browser and the REST API workshops using the same form:

https://docs.google.com/forms/d/e/1FAIpQLSd7GOl-aRfUTdTnMBVvdaZaSxPRYJbRwO7ood1Y00FNiTgsLA/viewform?usp=sf_link <https://docs.google.com/forms/d/e/1FAIpQLSd7GOl-aRfUTdTnMBVvdaZaSxPRYJbRwO7ood1Y00FNiTgsLA/viewform?usp=sf_link>
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