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Ensembl Browser Workshop

Gladstone and the Chan Zuckerberg Biohub are partnering to bring this 1-day workshop to our communities.
Thursday, January 25, 2018 - 9:30am to 5:00pm
Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158 (Yerba Buena Conference Room, 2nd Floor)

Course Overview

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Their sister project, Ensembl Genomes, can also be covered if participants are working with bacteria, plants, fungi, protists, or (invertebrate) metazoa. The workshop is primarily targeted at wet-lab researchers, and they customize the course for species of interest and to include total beginners to their browser up through frequent users.

Feedback

“There are probably quite a few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become.” —Browser workshop, CRUK, April 2016

“Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert.” —Browser workshop, Cardiff, March 2014

If you think you’d like to host a similar course at your institute, you can find out more on the Ensembl workshops page.


Audience

Wet-lab researchers and bioinformaticians


Learning Outcomes

Participants should be able to:

  • View genomic regions and manipulate the view to add features you are interested in
  • Explore information about genes and their sequences, and gene data in bulk using BioMart
  • Analyze genomic variants and associated phenotypes and your own variation data using the VEP
  • View homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types


Program

Morning: Introduction to Ensembl and Ensembl genes. Viewing genes and locations in the browser. Data export with BioMart.

Afternoon: The afternoon sessions depend on the participants’ interest. They can cover genetic variation, comparative genomics, and gene regulation, depending on what you express an interest in when you register.


Sample Program

9:30–10:15am Introduction to the Ensembl
10:15–11:00am Exploring Genomic Regions
11:00–11:20am Break
11:20am–12:15pm Exploring Genes and Transcripts
12:15–1:00pm Variation Data
1:00–2:00pm Lunch Break
2:00–2:30pm The Variant Effect Predictor
2:30–3:30pm Regulation Data
3:30–3:50pm Break
3:50–4:50pm Comparative Genomics
4:50–5:00pm Wrap-up and Feedback

Hosted By: 

Gladstone Institutes and the Chan-Zuckerberg Biohub


Biohub
499 Illinois Street
Yerba Buena Conference Room
Second Floor
San Francisco, CA 94158

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