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Fifth Course on Genome Browsing (2011): Access to Genes and Genomes with Ensembl-Biomart and the UCSC Genome Browser




The CNIO Bioinformatics Unit is organising a Fifth Course on Genome Browsing, to be held on Tuesday, November 15th 2011, and Tuesday, November 22th 2011.

The course is limited to 15 persons. Please contact us (This email address is being protected from spambots. You need JavaScript enabled to view it. This e-mail  address is being protected from spambots. You need JavaScript enabled to  view i) in advance if you wish to attend the course.




Access to Genes and Genomes with Ensembl-Biomart


Tuesday, November 15th 2011
Teacher: Giulietta Spudich, European Bioinformatics Institute (EBI)



Course Poster

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate sequences, with other species available in www.ensemblgenomes.org. This workshop offers  participants the possibility of gaining hands-on experience in the use  of the Ensembl Genome Browser and provides them with the necessary  background information. Primarily targeted at wetlab researchers, a  combination of hands-on exercises along with presentations will lead the  scientist through tools and annotation he/she may be able to use in the  course of biological research.










Course Agenda (Legado Clotilde Jiménez room, 3rd floor)
       
  • 9:00 Introduction   
  • 9:15 Worked example (walk-through of main pages of Ensembl)   
  • 10:45 Coffee break   
  • 11:15 Hands-on exercises (using the browser)   
  • 12:00 Introduction to BioMart (lecture and hands-on)   
  • 13:00 Lunch   
  • 14:30 Variations and Regulation  
  • 16:00 Coffee break   
  • 16:15 Comparative genomics
  • 17:30 Finish






Access to Genes and Genomes with UCSC  Genome Browser

Tuesday, November 30th 2010
Teacher: Osvaldo Graña, Bioinformatics Unit (CNIO)



Course Poster

The UCSC Genome Browser resource contains the reference (or official)  public DNA sequences and working draft assemblies for human and a large  collection of other genomes. There are a number of tools within it that  provide access to the sequences themselves, and many other useful genome  features to add context to the genomic information. Researchers can use  this site to find genes and gene predictions, expression information,  SNPs and variations, cross-species comparative data, and more.










Course Agenda (Legado Clotilde Jiménez room, 3rd floor)
       
  • 9:00 Introduction to UCSC Genome Browser (basic searches,  understanding displays)   
  • 9:45 Get details of sequences, sequence searches (BLAT), in  silico PCR, Proteome Browser, VisiGene Browser   
  • 11:00 Coffee break   
  • 11:15 Hands-on exercises (using the browser)   
  • 12:30 Gene Sorter   
  • 13:00 Lunch   
  • 14:00 Table Browser Introduction, Set up and filters,  intersections   
  • 14:45 Custom Tracks: Table Browser & User Generated   
  • 15:45 Coffee break   
  • 16:00 Summary   
  • 16:15 Hands-on exercises   
  • 17:30 Finish








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