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ISCBacademy Tutorial Series - Using the Ensembl genome browser and REST API to retrieve genome annotation data
Virtual Event

Hosted by: ISCBacademy
Venue: Virtual Event
Dates: Sep 28, 2023 through Sep 29, 2023

The Ensembl project provides freely available access to genome annotation datasets including gene, variant and regulatory feature annotation as well as comparative genomics analyses for over 300 vertebrate species and 30,000 non-vertebrate eukaryotes and prokaryotes. All of the data can be retrieved through Ensembl’s online genome browsers (www.ensembl.org, www.ensemblgenomes.org and rapid.ensembl.org) as well as programmatically via Ensembl’s REST API.

This workshop will introduce you to the range of data available through Ensembl and the appropriate platforms to visualise and extract it for analysis and interpretation. The morning sessions of this workshop will guide you through the Ensembl genome browser and BioMart interfaces to show you how to explore and retrieve both small and large-scale datasets. In the afternoon session, this workshop will introduce you to the concepts of the Ensembl REST API and guide you through the principles of retrieving Ensembl data programmatically using both Python and R.

To participate in the hands-on aspects of this workshop, including live polling, exploring online databases and exercises, you will need to bring a laptop. Workshop materials, including slides, screenshots, exercises, sample files and solutions will be available before the workshop and will remain permanently online at the Ensembl training portal: https://training.ensembl.org.

strongLearning objectives/strong
liOutline the different data types available through Ensembl/li
liIdentify the appropriate methods for data retrieval from Ensembl/li
liVisualise and retrieve genome annotation data through the online Ensembl genome browser/li
liExport custom datasets from Ensembl using the BioMart export tool/li
liPerform queries and extract data returned from the Ensembl REST API/li
strongMaximum number of participants/strong

strongIntended audience and level/strong
The workshop is aimed at new and existing Ensembl users, from both the wet-lab and bioinformatics communities. The workshop is designed to provide participants with a greater understanding of the data available through the Ensembl interfaces and how to efficiently retrieve it at various scales.
There are no prerequisites for this workshop, although a basic understanding of programming with Python or R would be beneficial. For the interactive aspects of this workshop, participants are required to bring their personal laptops.
Additional Information
Event URL: https://www.iscb.org/iscbacademy
ISCB Member Discount: TBA

While ISCB provides for conference and event listings that may be of interest to members and bioinformaticians at large, ISCB is not responsible for the content provided by outside sources. Such listings are not meant as an endorsement by ISCB.

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