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Ensembl Browser Workshop In-Person

This full-day workshop will provide an introduction to Ensembl (www.ensembl.org), a freely available project offering one of the most comprehensive and integrated genomic resources. We currently have over 80 vertebrate species, including human - our most highly accessed genome, whether in its latest assembly (GRCh38) or previous ones (GRCh37 and NCBI36). Our sister project, Ensembl Genomes expands this to over 40,000 bacterial, plant, fungal, protist and metazoan genomes.

 

Ensembl annotates genes and transcripts based on biological evidence, generates gene trees (both protein coding and non-coding) and whole genome alignments. To annotate other genomic features such as SNPs, CNVs and regulatory elements, Ensembl draws on major biological projects including; 1000 Genomes, ENCODE, Roadmap Epigenomics, and Blueprint epigenome. We also integrate data from many reference databases such as dbSNP, the NHGRI-EBI GWAS catalogue and OMIM. These data can be accessed through our web browser, APIs (Perl and REST), MySQL and FTP dumps, and our toolkit (e.g. our popular VEP, BioMart, BLAST/BLAT).

 

Depending on your interests, the workshop will cover the following topics on the Browser:

-Introduction to Ensembl: origin, goals and organisation of the Ensembl project

-Genebuild: how are Ensembl gene and transcripts predictions made?

-Data export with BioMart: building queries to access data in our databases, using a web interface (no programming required)

-Variation: SNPs and other polymorphisms, structural variants, the variant effect predictor

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

-Regulation: Sequences that may be involved in gene regulation

For each module, Helen Sparrow, an Ensembl Outreach Officer will give a presentation, a hands-on demonstration, followed by the opportunity to do exercises.

 

You are encouraged to bring your own research problems/questions, and try to tackle these during the workshop using Ensembl.

 

Helen joined Ensembl as an Outreach Officer in 2015. As a member of the Outreach Team she delivers workshops, answers helpdesk queries, creates training materials and help pages, and manages social media. Before starting at EMBL-EBI, Helen did her PhD in environmental biotechnology at the University of York, then worked as the community manager at academia.edu and as a trainee museum educator at the California Academy of Sciences.

Date:
Monday, Jan 23 2017
Time:
9:00am - 5:00pm
Time Zone:
Pacific Time - US & Canada (change)
Location:
Mission Hall 1406
Campus:
Mission Bay
Categories:
  Data Science > Bioinformatics and Statistics     Data Science  
Registration has closed.

Event Organizer

Profile photo of Ariel Deardorff
Ariel Deardorff

Data Services Librarian

ariel.deardorff@ucsf.edu