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.
We’ve got another round of our recurring virtual series covering the genome browser and the REST API. Both workshops will be held between Tuesday – Thursday, with the Browser on 7th-9th September and the REST API on 14th-16th September 2021 (2pm-5pm BST). Read on for more information and registration instructions.
Ensembl runs a regular series of open Browser and REST API workshops. Every other month, we offer either morning or evening times (BST) suited to different time-zones. Don’t worry if September time slots don’t work for you, there will be another round soon.
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
|Tuesday 7th September 2021, 2pm-5pm (BST)||Introduction to Ensembl.|
Ensembl Genes and Transcripts.
|Wednesday 8th September 2021, 2pm-5pm (BST)||Ensembl Variation and the Variant Effect Predictor (VEP).|
Comparative genomics in Ensembl.
|Thursday 9th September 2021, 2pm-5pm (BST)||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
|Tuesday 14th September 2021, 2pm-4:30pm (BST)||Overview of the REST API and how to query the REST API with URLs. Fetching REST endpoints programmatically.|
|Wednesday 15th September 2021, 2pm-4:30pm (BST)||Fetching specific data points from REST queries. Linking REST queries together.|
|Thursday 16th September 2021, 2pm-4:30pm (BST)||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.
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.