This course type is computational

Bioinformatics Summer School

13 - 17 June 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    This popular computational course is run jointly with EMBL-EBI and will
    provide an introduction to the use of bioinformatics in biological
    research using publicly available data resources and tools. Participants
    will initially be introduced to bioinformatics theory and practice.

    To enable the specific exploration of resources, in a particular
    field of interest, participants will actively take part in a
    project; working with others to conduct bioinformatics based research to
    explore biological questions. This group project is a major element of
    the course; participants will be placed into groups according to their
    scientific area of interest and relevance to available projects. The
    bioinformatics resources, available in their area of interest, will be
    explored and applied to a set problem. The group work will culminate in a
    presentation session involving all participants on the final day of the
    course, giving an opportunity for wider discussion on the benefits and
    challenges of working with biological data.

    This course is aimed at individuals working in biological disciplines who
    have little or no experience in bioinformatics. Applicants are expected
    to be beginning bioinformatics related projects or need to use such
    approaches in their work.

    Please note: The course will not cover aspects of
    computer programming or in-depth data analysis; there will be no
    opportunity for you to analyse your own data during this course.

    Learning outcomes
    Following course completion participants should be able to:

    • Discuss applications of bioinformatics in biological research
    • Browse, search, and retrieve biological data from public repositories
    • Use appropriate bioinformatics tools to explore biological data
    • Comprehend some ways biological data can be stored, organised and interconverted
  • Programme

    The Bioinformatics Summer School 2016 will start at
    approximately 10.00 on Monday 13 June and close at approximately 14.30 on
    Friday 17 June 2016.

    This is a residential summer school. All students are requested to stay
    onsite for the full duration to benefit fully from discussions and
    interactions with the faculty and other students. The programme will
    include training and mentoring provided by experts from EMBL-EBI and
    external institutes.

    Course topics

    • Issues in bioinformatics
    • Designing bioinformatics studies
    • Databases
    • Tools


    Group projects
    Participants will be divided into focused groups to work on a small
    project set by EMBL-EBI resource and research staff, ending in a
    presentation from each group on the final day of the course. In your
    application you should indicate which of the following projects would
    most benefit your research:

    • De novo assembly and annotation: Participants will assemble and annotate the genome of a strain of Escherichia coli. Compare the results to known genomes to discover why this strain, of mainly harmless bacteria, turned out to be deadly.
    • Phylogenetics: Investigation of a dataset of viral sequences and the use of various phylogenetic analyses to draw conclusions about the evolutionary history of the taxon and its geographic spread.
    • RNA-Seq and networks: This project will investigate expression changes, associated with glioblastoma, using expression data obtained from normal and tumour tissue. The focus of this project will be how expression levels are different in cancer.
    • Structural biology and functional prediction: Investigation and prediction of the functions of uncharacterised proteins, using PDBe’s search interface. As part of the project you will develop a workflow and access PDBe programmatically via an API.
    • Chemogenomics: This project will involve target-ligand pairs, SureChembl for patent disease data, KNIME for data analysis and PDB for study of protein-ligand interactions. Some docking calculations may be performed to determine potential ligands for the identified target

    During the application process you will be required to select which of
    the above projects would benefit your research most. Additional
    alternative projects may be made available if high interest is shown in a
    particular area of research not currently reflect above. This can be
    detailed in “other” during the application process.

    A draft programme will be available shortly.

  • Instructors / Speakers

    Course instructors 
    Sarah Morgan EMBL-EBI, UK

    Laura Emery EMBL-EBI, UK
    William Pearson University of Virginia, USA
    Tom Hancocks EMBL-EBI

    Keynote lecture
    Julian Rayner Wellcome Trust Sanger Institute, UK

    Confirmed tutors
    Andrew Cowley
    EMBL-EBI, UK
    William Pearson University of Virginia, USA
    Pedro Beltrao EMBL-EBI, UK

    Event organiser
    Lucy Criddle Wellcome Genome Campus, UK

  • How to Apply

    Fees

    Registration with Single Accommodation  £600

    The fees include accommodation, meals and lectures for the duration of
    the Bioinformatics Summer School 2016. The fee will be requested once
    acceptance is confirmed.

    Accommodation
    This is a residential summer school. All participants will stay at The
    Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, for the
    nights of 13, 14, 15 and 16 June 2016.

    If you wish to book onsite accommodation either side of the summer
    school/course dates, please contact the Conference
    Centre
    directly.

    Applications
    Application deadline: Closed

    Places on this summer school are limited to 30 students and will be
    awarded on merit. Applicants should be PhD students currently engaged in
    relevant research and will be required to complete an online application
    form.
    The selection process will take place in March 2016

    The following will need to be provided:

    • Qualifications and justification for attendance
    • A list of relevant publications
    • A scientific outline of current research
    • Supervisor’s details: your supervisor will then receive an e-mail requesting a supporting statement to complete your application.

    Please note: Applications cannot be considered without a
    supervisor’s supporting statement.

    Travel visas
    Please contact the event organiser if you require a letter to support a
    travel visa application, once your application has been successful. Note
    that letters will be provided to confirmed attendee only.

    Non-European Economic Area or Swiss nationals may be required to have a
    visa to enter the UK.
    Early application is strongly advised, as this process can take 6-8 weeks
    or longer.

    Please visit the following websites for further information:
    UK Border Agency website:
    www.ukba.homeoffice.gov.uk/visas-immigration/
    Information for general visitors and business visitors:
    www.ukba.homeoffice.gov.uk/visas-immigration/visiting/business/business-activities/