Ensembl Genome Browser Workshop — January 26, 2018

Posted by & filed under Training.

The Bioinformatics Core and the Shields Library are hosting an Ensembl Genome Browser Workshop on January 26!

For more information and to register, go to https://registration.genomecenter.ucdavis.edu/.

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).

Topics will include:

  • 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)

he 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

This workshop will be held in a computer classroom at Shields Library and will run from 9:30am to 5:00pm on January 26, 2018. You may either use one of the MS Windows desktops or you may bring your own laptop to use.

There is a registration fee of $40, which includes all workshop materials. Coffee and snacks will also be provided.

For more information and to register, go to https://registration.genomecenter.ucdavis.edu/.