Sign up for our virtual series covering the Ensembl genome browser and accessing Ensembl data via its REST API. Both workshops will be held from Tuesday to Thursday, with the browser course running from 10th to 12th October and the REST API course from 17th to 19th July (09:00 – 12:00 BST). Read on for more information and how to register.
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, 10th October 2023 09:00 – 12:00 (BST) | Introduction to Ensembl Ensembl Genes and Transcripts |
| Wednesday, 11th October 2023 09:00 – 12:00 (BST) | Ensembl Variation and the Variant Effect Predictor (VEP) Comparative genomics in Ensembl |
| Thursday, 12th October 2023 09:00 – 12:00 (BST) | Features that regulate gene expression Custom export of Ensembl data with BioMart |
Ensembl REST API workshop
The Ensembl REST API workshop is aimed at researchers and developers interested in exploring Ensembl data beyond the website. The workshop covers how to access Ensembl data via its 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. Please note that 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, 17th October 2023 09:00 – 12:00 (BST) | Overview of the REST API and how to query the REST API with URLs Fetching REST endpoints programmatically |
| Wednesday, 18th October 2023 09:00 – 12:00 (BST) | Fetching specific data points from REST queries Linking REST queries together |
| Thursday, 19th October 2023 09:00 – 12:00 (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. A Zoom meeting link and further information will be sent to participants upon registration.
On each day, two modules plus interactive exercise sessions will be covered, with short breaks in-between.
You will be able to ask the instructors questions during the workshops, 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 Ensembl REST API workshops using the same form:
If you have any questions, please do not hesitate to contact the Ensembl Helpdesk.