UC San Diego Ensembl Tutorial workshop

The Cancer Cell Map Initiative (CCMI) is a cross-campus research program lead by Prof. Trey Ideker (UC San Diego) and Prof. Nevan Krogan (UCSF). The CCMI is leveraging advanced interaction mapping and computational capabilities to generate, assemble and analyze cancer networks, focusing initially on head and neck squamous cell carcinoma and breast cancer. The CCMI is a proud member of the NCI’sCancer Systems Biology Consortiumwith additional funding provided by theRoddenberry Foundationand the Fred B. Luddy Foundation.Join the CCMI mailing list to receive notice of upcoming events.

The Cancer Cell Map Initiative

Hosted by Erin Haskell, Ensembl Outreach Officer from the <A HREF="https://www.ebi.ac.uk/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">EMBL-EBI</A>.
This full-day workshop will provide an introduction to the Ensembl genome browser (<A HREF="http://www.ensembl.org/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">www.ensembl.org</A>), 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 (<A HREF="http://www.ensemblgenomes.org" TARGET="_blank" TITLE="http://www.ensemblgenomes.org" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">www.ensemblgenomes.org</A>), 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 40 attendees.   
 
Schedule
<UL>
<LI>09:30 – Introduction to Ensembl</LI>
<LI>10:00 – Exploring the Genome Browser</LI>
<LI>11:00 – Coffee break</LI>
<LI>11:15 – Genes and transcripts</LI>
<LI>12:15 – BioMart</LI>
<LI>1:00 – Lunch</LI>
<LI>2:00 – Variation and the VEP</LI>
<LI>3:45 – Coffee break</LI>
<LI>4:00 – Compara or Regulation</LI>
<LI>5:15 – Wrap up, feedback, and questions</LI>
</UL>
 
<HR>
 
Directions
Parking at UC San Diego requires a valid permit. Hourly rates are posted at pay stations; credit cards are accepted. A map of the MET Building and nearby parking lots can be viewed <A HREF="https://maps.ucsd.edu/map/?id=1005&mrkIid=163135" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">here</A>. The nearest parking lots include Osler Parking Structure, Gilman Parking structure, and lots P602 or P603. If using the UC San Diego Shuttle, exit at Gilman Dr and Meyers Ln, then walk south towards School of Medicine.
 
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.

UC San Diego

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UC San Diego Ensembl Tutorial workshop

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