Human and Vertebrate Genomics: Bioinformatics Tools and Resources (Montevideo, Uruguay)

12 - 16 September 2016Montevideo, Uruguay
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This 5-day course provides an intensive introduction to bioinformatics
    tools freely available on the internet, focusing primarily on the Human
    Genome data. Students will be given hands-on training in the use of
    public databases and web-based sequence analysis tools. All course
    materials will be provided and also made available on the Web.

    The course has a strong emphasis on applied training, and practical
    exercises along with interaction and discussion between students and
    instructors are key features of the programme. Each student will have
    access to a desktop PC for the duration of the course.

    This course is limited to 20 participants from Latin America and the
    Caribbean.
    Please note:
    The course will be taught in English.

    Learning Outcomes:
    By the end of this course, participants will be able to:

    • Browse and query genomes, and be able to interpret how genes and other features are displayed. Download data with BioMart and Table browser, upload their own data and interpret different biotypes.
    • Identify paralogous and orthologous genes, compare genomes and identify evolutionary conserved sequences.
    • Explore and interpret ENCODE data.
    • Query protein and domain databases, interpret protein structures, perform basic homology modelling and investigate pathway databases.
    • Access non-coding RNA databases, microRNA resources and view and interpret them.
    • Query genomic variation resources, integrate variation information and view this in the context of the genome and interpret genotypes and haplotypes.
    • Explore variation and the relationship between genotype, phenotype and disease using a variety of tools and databases.
    • Evaluate Next Generation Sequencing methods and their applications.
  • Programme

    The programme will include lectures and practical, computer-based
    sessions covering the following topics:
    (View
    the full list of resource URLs here
      |  View
    the draft timetable here
    )

    Genome Browsing:

    • Ensembl
    • VEGA
    • UCSC

    Comparative Sequence Analysis:

    • Homologous gene identification – Paralogues and Orthologues
    • Ensembl – orthologue prediction, MultiContigView
    • NCBI Gene – BLink, Homologene
    • Comparative Genome Analysis – UCSC, ECR browser

    Working with Encode Data:

    • Epigenetics
    • ENCODE project
    • ENCODE portal
    • Browsing ENCODE data with UCSC
    • Browsing ENCODE data with Ensembl
    • Ensembl Regulatory Build

    Proteins, Complexes and Pathways:

    • UniProt
    • InterPro/Pfam protein
    • PDBe/PDBSum
    • IntAct
    • Reactome/Metacyc

    non-coding RNA:

    • Rfam
    • MicroRNA/targets
    • lncRNA db and Vega
    • RNACentral

    More Complex Genome Browsing:

    • Ensembl Biomart
    • UCSC Table Browser
    • Uploading your own data

    Genomic Variation:

    • Ensembl SNP information, Geneview in dbSNP
    • Genotyping
    • Haplotypes and HapMap
    • Haploview

    Variation, Function and Disease:

    • Polyphen, SIFT
    • Ensembl VEP
    • OMIM
    • COSMIC
    • DECIPHER
    • GEO
    • ONTOLOGIES
  • Instructors / Speakers

    Course instructors
    Jane Loveland Wellcome Trust Sanger Institute
    Simon Gregory Duke University
    Ben Moore The European Bioinformatics Institute
    Matt Clark The Genome Analysis Centre
    Pablo Rabinowicz Independent Consultant
    Bert Overduin Edinburgh Genomics, The University of Edinburgh

  • How to Apply

    Prerequisites
    The course is open to research scientists based in institutes anywhere in
    Latin America and the Caribbean (including laboratory and clinical staff
    as well as specialists in related fields). Applicants should have a
    minimum of a degree in a biological discipline.

    Cost
    Overseas courses are free to attend for non-commercial applicants.

    Applications
    Applications for this course can be completed online. If you have any
    problems with the online application process, please contact us.

    Please note: Applications
    must be supported by a
    recommendation from a scientific or clinical sponsor (e.g. supervisor or
    head of department). A request for a supporting
    statement will be sent
    to your nominated sponsor automatically during
    the application process.
    Applicants must ensure that their sponsor
    provides this supporting
    statement by the application deadline. Applications without a supporting
    statement cannot be considered.

    Deadlines
    Deadline for Applications: Closed

  • Bursaries

    Bursaries
    Overseas courses are free to attend for non-commercial
    applicants. Limited bursaries to cover travel, accommodation and
    sustenance costs are available and are awarded on merit. If you would
    like to apply for a
    bursary, please complete the bursary section of the
    online application
    form.

    Please note that both the applicant
    and sponsor are required to provide
    a justification for the
    bursary as part of the application

    Bursary terms and conditions

    UK Courses (held at the Wellcome Genome Campus, Hinxton,
    Cambridge)
    A
    limited number of bursaries are available for each course. These are
    awarded by the selection committee according to merit. The bursary
    covers a maximum of 50% of the course fee, though in exceptional
    circumstances an application for the total course fee may be considered.
    Where there are many bursary applications, the selection committee may
    issue smaller amounts. We cannot assist with travel costs to attend UK
    courses.

    Overseas Courses (held outside of the UK)
    A
    limited number of bursaries are available for each course. These are
    awarded on merit to cover travel, accommodation and sustenance. The
    maximum award for travel (economy class) will be £750.

    Bursaries can be applied for as part of the course application form.
    Applicants
    will be notified of a bursary award along with their place on
    the
    course, usually within one month of the application deadline. The
    decision of the selection committee is
    final.