R4Bioinfo Workshop: Introduction to Ensembl REST API - PART1

We are delighted to get back to the R4Bioinfo series that we've launched in September 2020. We will be organizing a series of two workshops about Introduction to Ensembl REST API.

Date/Time: Friday, June 4th, 2021 from 6 PM to 8:15 PM (GMT+1)
Place: ZOOM

▶️ Invited trainer: Dr. Aleena Mushtaq and Dr. Michal Szpak

▶️ About Dr. Aleena Mushtaq:
Aleena’s background is in Biomedical and Molecular sciences. She completed her PhD in 2020 at the University of East Anglia, UK. For her doctorate she studied the dynamic relationship of host and microbiota in the gut-liver axis in response to Western diets. She joined EMBL-EBI as an Ensembl Outreach Officer in 2021 and delivers training on Ensembl resources.

▶️ About Dr. Michal Szpak:
Michal took a degree in biology at the University of Warsaw, where he
studied ancient DNA. He subsequently moved to bioinformatics and
explored human genetic variation across different ethnicities in his
master’s degree research at the Center for Public Health Genomics,
university of Virginia. He joined the human evolution team at the
Wellcome Sanger Institute in 2012 and received his PhD in human
population genetics from University of Cambridge. His doctoral and
postdoctoral work at the Sanger focused on positive selection and
genetic adaptations in humans. He joined EMBL-EBI as an Ensembl Outreach Officer in 2019 and continues to deliver Ensembl training worldwide.

▶️ About the workshop:
This workshop will be divided into two parts. During these two parts you'll learn about:

• Introduction to REST API
• Making requests with R
• Find an endpoint which you can use to lookup information about a gene using its symbol
• Create a URL to find information about a gene
• Expand your results to include information about transcripts
• Convert a fromJSON module used to pull out the data to a dataframe
• Get a sequence in FASTA
• Gene trees and homologues in various formats
• Alignments
• Get all variants that are associated with a phenotype and print the needed information about these variants
• Linking endpoints together
• Using POST to run a query with multiple inputs at once

▶️ Requirements of the workshop:
The Ensembl REST API workshop requires familiarity with the Ensembl Browser and data structure. You can find an online version of the Ensembl Browser workshop with exercises here (https://www.ebi.ac.uk/training/online/courses/ensembl-browser-series/). The invited trainers will go over these materials (http://training.ensembl.org/events/2021/2021-06-04-RLadiesREST_June) during the training session.

By the end of this series, you will be able to make requests with R through Ensembl REST API.

In order to attend the event, please fill out this form 👉
https://tinyurl.com/judj2az8

We will send you the ZOOM link a few hours before the training session. Please check out your email later.

We look forward to welcoming you!