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1st Course on Genome Browsing

The CNIO Bioinformatics Unit organises a first Course on Genome Browsing, to be held on Tuesday, December 18th 2007, and Wednesday, December 19th. It will cover theoretical and practical aspects on using Ensembl, Biomart and UCSC Genome Browser.

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. ) in advance if you wish to attend the course.  Keep reading to check the course contents.

Access to Genes and Genomes with Ensembl-Biomart

Tuesday, December 18th

  • Teacher: Giulietta Spudich, European Bioinformatics Institute (EBI)

The Ensembl project provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. 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 (CNIO Seminars 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 The Ensembl Gene Set
  • 15:00 Hands-on exercises, using Ensembl Genes
  • 16:00 Coffee break
  • 16:15 Case study with a gene of interest

Access to Genes and Genomes with UCSC Genome Browser

Wednesday, December 19th 

  • Teacher: Osvaldo Graña, Bioinformatics Unit (CNIO)

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 (CNIO Training room, 1st 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 Case study with a gene of interest
           [First part material] [Second part material]

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