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UCSF Ensembl Tutorial workshop

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Gladstone Institutes

Conference Room A/B

1650 Owens Street

San Francisco, CA 94158

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Description

Hosted by Erin Haskell, Ensembl Outreach Officer from the EMBL-EBI.

This full-day workshop will provide an introduction to the Ensembl genome browser (www.ensembl.org), a freely available comprehensive and integrated genomic resource. Ensembl currently has over 130 vertebrate species available, including human genomes, whether in its latest assembly (GRCh38) or the previous versions (GRCh37 and NCBI36). The database additionally includes 14 popular laboratory mouse strains. Our sister project, Ensembl Genomes (www.ensemblgenomes.org), contains an additional 45,000 bacterial, fungal, metazoan, plant, and protist genomes.

Ensembl annotates genes and transcript models 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. VEP, BioMart, BLAST/BLAT).

The only prerequisite for this workshop is general knowledge of molecular biology and genomics, and a laptop with a web browser. Due to the hands-on format of this workshop, attendance is limited to 35 attendees.

Schedule

  • 09:00 – Introduction to Ensembl
  • 09:30 – Exploring the Genome Browser
  • 10:30 – Coffee break
  • 10:45 – Genes and transcripts
  • 11:45 – BioMart
  • 12:30 – Lunch
  • 01:30 – Variation and the VEP
  • 03:15 – Coffee break
  • 03:30 – Compara or Regulation
  • 04:45 – Wrap up, feedback, and questions




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. A no-show may limit your ability to book our events in the future. Thank you for your understanding.

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Date and Time

Location

Gladstone Institutes

Conference Room A/B

1650 Owens Street

San Francisco, CA 94158

View Map

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