Working with Parasite Database Resources (Montevideo, Uruguay)

16 - 21 October 2016Montevideo, Uruguay
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This week-long course aims to provide experimental biologists working on
    eukaryotic pathogens 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 (including
    the EuPathDB search strategy system).

    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). One important aspect is for the participants
    to understand the origin of the underlying data in the databases and how
    to analyse it. Applicants working on any organism included in 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 (a multi-centre collaborative
    effort including the Universities of Georgia & Pennsylvania in the US
    and Liverpool in the UK). The majority of this intensive course will be
    based on hands-on exercises with lectures on genomics and bioinformatics
    techniques, in addition to keynote presentations by distinguished guest
    speakers.

    Please note: The course is open to scientists and
    clinicins based in Latin American and Carribean institutes and there is
    no fee to attend. Bursaries are available to cover travel and
    accommodation expenses. There are 20 places available and the course will
    be taught in English.

    Feedback from the 2015 course

    -The atmosphere encourages learning and I love that aspect so much.
    Thank you for all of this.
    -I would really like to thank all the instructors for this useful
    workshop. The course structure was really well planned.
    -Thank you very much for organizing this wonderful training.
    -Thank you very much for running this course. It’s been absolutely
    fantastic and I really have learned how to use a
    huge repertoire of tools. It’s also been a fantastic thing to meet and
    mingle with members of the parasitology
    community and to experience different cultures and attitudes to
    learning.

  • 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 and GO enrichment analysis
    • Working with next-generation sequence data (mapping, variant calling, RNA-Seq etc)
    • An introduction to community curation tools
    • Participants are encouraged to bring own data, to use in consultation and/or in-workshop analysis.

    Learning outcomes
    After attending this course, participants should be able
    to:

    • Comfortably work with state-of-the-art bioinformatics software both using online resources as well as in a UNIX-like environment
    • Have a good understanding of the application, opportunities, visualization and analysis of next generation sequencing datasets for parasitology research
    • Integrate and query large-scale genomic and functional genomic databases to answer biology-related research questions and develop testable hypotheses
    • Use software and web-based services to browse genomes, visualise next generation data and display genome comparisons.
  • Instructors / Speakers

    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 (a multi-centre
    collaborative
    effort including the Universities of Georgia &
    Pennsylvania in the
    US and Liverpool in the UK).

    The majority of this
    intensive course will be based on hands-on
    exercises with lectures on
    genomics and bioinformatics techniques, in
    addition to keynote
    presentations by distinguished guest speakers.

    Guest speakers will be announced shortly.

  • How to Apply

    Prerequisites
    Applicants
    should be scientists or clinicians based in institutes in
    Latin America or the Carribean and should be
    actively involved in, or
    soon to commence, relevant research. Please note that
    the course will be taught in English.

    Cost
    Overseas courses are free to attend for non-commercial applicants.
    Additional bursaries are available for travel and accommodation expenses
    (see “Bursaries” tab).

    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: 17 June 2016

  • 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.