This course type is computational

Working with Parasite Database Resources

18 - 23 October 2015Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This residential workshop aims to provide experimental biologists working
    on protozoan parasites with hands-on experience in genomic-scale data
    analysis, including genome browsers and comparison tools, methods for
    data integration, and resources for sophisticated data mining. Examples
    and exercises will be drawn primarily from the EuPathDB.org and GeneDB.org
    resources and will include a variety of eukaryotic parasitic organisms
    including Apicomplexa (ie. Plasmodium and Toxoplasma)
    and kinetoplastida (ie. Trypanosoma and
    Leishmania). Applicants working on any protozoan parasite from
    these resources will benefit.

    This course is taught as a collaborative effort between the Parasite
    Genomics Group (Wellcome Trust Sanger Institute, UK) and the Eukaryotic
    Pathogen Bioinformatics Resource Center (University of Georgia &
    University of Pennsylvania, US). The majority of this intensive programme
    will be based on hands-on exercises with lectures on genomics and
    bioinformatics techniques, in addition to daily keynote presentations by
    world-renowned parasitologists.

    Feedback from the 2014 workshop
    “Thank you for this wonderful course!”
    “The workshop was really amazing! It gave to me the opportunity to
    investigate in deep some aspects of my research in a very simple way. The
    instructors were all very competent and friendly.”
    “It was a great experience!! I learnt a lot, discovered stuff hands-on
    and am taking an amazing experience back with me, to my work and
    life!!”

  • Programme

    The programme will include lecture and practical computational sessions
    covering the following topics:

    • Visualisation of sequence features and next generation sequencing data using the Artemis genome browser and annotation tool
    • Genome browsing and comparative genomics (ACT, J/GBrowse, SynView)
    • Formulating complex biological queries in computationally accessible form
    • Web-based resources including the GeneDB.org and EuPathDB.org family of databases
    • Integrating functional genomics data (RNA-seq, ChIP-seq, ChIP-chip, microarrays, proteomics, etc) with genome sequence data
    • Theoretical aspects of genome re-sequencing
    • Querying genetic diversity on a genome-wide scale
    • Metabolic pathways and pathway analysis, and compounds
    • Working with next-generation sequence data (mapping, variant calling, etc)
    • An introduction to community curation tools
    • Special topics of particular interest to workshop participants (participants will be polled on material they would like to see discussed).
  • Instructors / Speakers

    Instructors
    The workshop is taught as a collaborative effort between the Parasite
    Genomics Group (Wellcome Trust Sanger Institute, UK) and the Eukaryotic
    Pathogen Bioinformatics Resource Center (University of Georgia &
    University of Pennsylvania, US).

    Guest speakers
    Kirk W. Deitsch Weill Cornell Medical College, USA
    Mohamed-Ali Hakimi INSERM, France
    Ross Waller University of Cambridge, UK

  • How to Apply

    Prerequisites
    Applicants should have a minimum of a degree in a biological discipline
    and be actively involved or soon to commence relevant research.

    Cost
    The
    course is subsidised by the Wellcome Genome Campus
    Advanced Courses and Scientific Conferences Programme. This is a
    residential
    course and there is a fee of £525 towards board and lodging
    for non-commercial applicants. Please contact us for the commercial fee.

    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
    UK: Advanced Courses are subsidised for non-commercial
    applicants from anywhere in the world. Additional, limited bursaries are
    available (up to 50% of the course fee) 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.