Exploring Genomes with Ensembl Beta

About the workshop

( https://beta.ensembl.org/) provides a new Ensembl interface and infrastructure for accessing genomic information, including genes, variants, comparative genomics and gene regulation data for over 3000 species from across the tree of life.

This workshop will provide participants with the opportunity to learn about the wide range of data available through Ensembl and gain hands-on experience in navigating the Ensembl website to retrieve and interpret data.

The workshop consists of a series of modules which include a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl. The Ensembl Beta is in active development, so expected features may not be available or will change in the near future. Feedback on the site and how it meets your needs will form part of the workshop.

Target Audience

This is an introductory workshop that is aimed at wet-lab scientists and bioinformaticians who are new to using Ensembl or have not yet discovered the power and depth of this resource. For the interactive aspects of this workshop, participants are encouraged to bring their personal laptops.

Learning Objectives

• Access the main data types through the Ensembl web browser platform: genomes, genes, genetic variation; and an outline of regulatory features and homology annotation
• View genomic regions from chromosomal to nucleotide scale
• Explore information about genes and their sequences
• Analyse genomic variants using the Variant Effect Predictor (VEP)
• View homologous genes across species reference collections
• View functional elements involved in gene regulation alongside gene transcripts
• Outline accessing data at whole genome scales or via programmatic means

Ensembl Outreach

The Ensembl Outreach team and Ensembl are part of the European Bioinformatics Institute (EMBL-EBI), who provide open-access bioinformatics resources and training to researchers around the globe. The workshop will be delivered by Jorge Batista da Rocha, who completed his PhD in Bioinformatics and Human Genetics at the University of the Witwatersrand, South Africa. Refreshments provided courtesy of the Cancer Cell Map Initiative ( http://ccmi.org/)

Schedule

• 9:00 AM Workshop Begins
• 12:00 PM Workshop Ends
• 12:00 - 1:00 PM Lunch

Lunch and refreshments will be provided

Directions: Parking at UC San Diego requires a valid permit. Hourly rates are posted at pay stations or use the Park Moblie App. Nearest parking locations include the South Parking Structure, the Gilman Parking Structure, and parking lots P602 and P603.

If using the UC San Diego Shuttle, exit at Gilman Dr and Meyers Ln, then walk south towards School of Medicine. Google Map: https://goo.gl/maps/k26pZNPhVfbHgLp19

No Show Policy If you are unable to attend for any reason, please cancel your registration at least two business days prior to the event. Your cooperation ensures our programs can be made available to interested attendees and remain fiscally sustainable. Repeated no-shows may limit your ability to attend our events in the future. Thank you for your understanding.

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