Ensembl Browser Workshop Jan 2020

This workshop is jointly hosted by the Shields Library and the Genome Center Bioinformatics Core.

The Ensembl and Ensembl Genomes projects (www.ensembl.org) provide a comprehensive and integrated source of annotation of vertebrate and non-vertebrate genome sequences, respectively. The browser workshop will include presentation and demonstration, and provide participants an opportunity to gain hands-on experience in the use of Ensembl genome browsers. Depending on the preferences of the participants, more or less emphasis can be allocated to the Ensembl browser (vertebrates) and to the Ensembl Genomes browser (non-vertebrates). Preferences will be determined through a pre-course survey of registrants. The Ensembl browser workshops typically consist of the first four core modules below, plus one other module (Comparative Genomics or Regulation). The additional module will be determined by the pre-course survey in the following pages.

Core Modules:

• Introduction to Ensembl: origin, goals and organisation of the Ensembl project
• Genebuild: how are Ensembl gene and transcripts predictions made?
• Data mining with BioMart: retrieving genomic information using a web interface (no programming required).
• Variation: SNPs and other polymorphisms, haplotypes, structural variants like CNVs and the Ensembl VEP (variant effect predictor)

The final module will be selected from the options below, based on pre-course survey:

• Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions

OR

• Regulation (Human and Mouse): Finding sequences that may be involved in gene regulation, and integration of ENCODE, Roadmap Epigenomics and Blueprint data

Prerequisites: The only prerequisite for this workshop is general knowledge of molecular biology and genomics and a familiarity with web browsers.

What do I need to bring? … This workshop will be held in a computer classroom at Shields Library. If you want to bring your own laptop to use, it will need to be able to run a current web browser, such as Chrome or Firefox.

Can I bring my own data? … No, but we will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How  much does it cost? … The registration fee is $50, which covers the cost of hosting the workshop.

Where is the workshop? … This workshop will be held in a computer classroom at Shields Library and will run from 9:30am to 5:00pm on Thursday January 23. Coffee and snacks will be provided.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible to ensure your place in the workshop!

Where can I find more information, including your policies?  ... Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ.

Questions?

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu