gravatar for Michal @Ensembl

2 hours ago by

UK, Cambridge, EMBL-EBI

Ensembl is hosting free virtual workshops covering the genome browser and the REST API. The Browser workshop will be held between Tuesday 16th March – Thursday 18th March 2021 (9am-1pm) and the REST API workshop will be held between Tuesday 23rd March – Thursday 25th March 2021 (9am-11:30am).

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
  • Visualise your own data in the Ensembl genome browser

Schedule:

  • Tuesday 16th March 2021, 9am-1pm (GMT): Introduction to Ensembl,
    Ensembl Genes and Transcripts.
  • Wednesday 17th March 2021, 9am-1pm (GMT): Ensembl Variation and the
    Variant Effect Predictor (VEP), Comparative genomics in Ensembl.
  • Thursday 18th March 2021, 9am-1pm (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 scripts to access data via the Ensembl REST API

Schedule:

  • Tuesday 23rd March 2021, 9am-11:30am (GMT): Overview of the REST API
    and how to query the REST API with URLs, Fetching REST endpoints
    programmatically.
  • Wednesday 24th March 2021, 9am-11:30am (GMT): Fetching specific data
    points from REST queries. Linking REST queries together.
  • Thursday 25th March 2021, 9am-11:30am (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.



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