Open: Ensembl Browser and REST API virtual workshops

Registration is now open for two free virtual Ensembl workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 26th January – Thursday 28th January 2021 (2pm-5pm) and the REST API workshop will be held between Wednesday 3rd February – Friday 5th February 2021 (2pm-4:15pm). More information and registration instructions can be found below.

Update: registration is now closed as all of the available places on the virtual Ensembl browser and REST API workshops have been filled. If you would like to be added to the waiting list, please e-mail the Ensembl Helpdesk.

The Ensembl Browser workshop

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

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

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

Schedule:

Tuesday 26th January 2021, 2pm-5pm (GMT)Introduction to Ensembl.
Ensembl Genes and Transcripts.
Wednesday 27th January 2021, 2pm-5pm (GMT)Ensembl Variation and the Variant Effect Predictor (VEP).
Comparative genomics in Ensembl.
Thursday 28th January 2021, 2pm-5pm (GMT)Features that regulate gene expression. Custom export of Ensembl data with BioMart.

The Ensembl REST API workshop

The Ensembl REST API 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 Python/R scripts to call them. It is important to note that this course will not introduce you to the Ensembl browser and data types or provide an introduction to programming in Python or R. Proficiency in Python or R and attendance at an Ensembl 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/Perl scripts to access data via the Ensembl REST API

Schedule:

Wednesday 3rd February 2021, 2pm-4:15pm (GMT)Overview of the REST API and how to query the REST API with URLs. Fetching REST endpoints programmatically.
Thursday 4th February 2021, 2pm-4:15pm (GMT)Fetching specific data points from REST queries. Linking REST queries together.
Friday 5th February 2021, 2pm-4:15pm (GMT)Bulk REST API queries with POST. Other data types 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.

Registration

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

If you have any questions, please do not hesitate to contact the Ensembl Helpdesk.

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