This course type is computational

Proteomics Bioinformatics

04 - 09 December 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    Run jointly with EMBL-EBI, this
    course provides hands-on training in the basics of mass spectrometry and
    proteomics bioinformatics, search engines and post-processing software,
    quantitative approaches, MS data repositories, the use of public
    databases for protein analysis, annotation of subsequent protein lists
    and incorporation of information from molecular interaction and pathway
    databases.

    The course is aimed at research scientists with a minimum of a degree in
    a biological discipline, including laboratory and clinical staff, as well
    as specialists in related fields. The practical elements of the course
    will take raw data from a proteomics experiment and analyse it.
    Participants will be able to go from MS spectra, to identifying peptides
    and finally to lists of protein identifiers that can be analysed further
    using a wide range of resources. The final aim is to provide attendees
    with the practical bioinformatics knowledge they need to go back to the
    lab and process their own data (including large datasets) when
    collected.

    Learning Outcomes
    After completing the course, participants should be able to:

    • Use and understand bioinformatics tools to analyse shotgun proteomics data, involving identification and quantification approaches
    • Browse, search, submit and retrieve proteomics data from widely used public repositories
    • Discuss standards in proteomics bioinformatics and recognise its importance
    • Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
    • Use tools to perform functional annotation of lists of proteins


    Feedback from the 2015 course

    • “Thank you to all involved for making the course run so smoothly AND in such a logical progression. The course structure was very well conceived.”
    • “Thanks for the helpful and informative experience and this major milestone in my educational record alongside my PhD studies! You are the best :)”
    • “I think this course is very well organized, with top speakers! Every one of the speakers was available for Q&A, which is great. Overall, the course provides all the tools necessary for carrying your proteomics project and even gives you new ideas about all you could do. Thanks!”
    • “This is the best course that I have attended. Well done to the organizers and lecturers!”
  • Programme

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

    • Mass Spectrometry Basics
    • MS Search Engines and post-processing software
    • Quantitative proteomics
    • Protein sequence databases and their use
    • Protein sequence data in UniProt
    • Post-translational modifications
    • Standardisation of proteomics data
    • MS proteomics repositories and the ProteomeXchange consortium
    • PRIDE and PRIDE-related tools
    • Proteogenomics
    • Protein interaction data through IntAct and the IMEX consortium
    • Functional analysis of proteins using Cytoscape
    • Placing proteins in pathways using Reactome

    Learning Outcomes
    After completing the course, participants should be able to:

    • Use
      and understand bioinformatics tools to analyse shotgun proteomics data,
      involving identification and quantification approaches
    • Browse, search, submit and retrieve proteomics data from widely used public repositories
    • Discuss standards in proteomics bioinformatics and recognise its importance
    • Evaluate the strengths and weaknesses of several experimental and bioinformatics analysis approaches
    • Use tools to perform functional annotation of lists of proteins
  • Instructors / Speakers

    Scientific Organising Committee
    Juan A.
    Vizcaíno
    EMBL-EBI, UK
    Lennart
    Martens
    Ghent University and VIB, Belgium
    Annalisa Mupo
    EMBL-EBI, UK

    The course will be taught by trainers from the
    European Bioinformatics
    Institute.

    Guest speakers
    Jyoti
    Choudhary
    Wellcome Trust Sanger Institute, UK
    René P.
    Zahedi
    Leibniz – Institut für Analytische Wissenschaften – ISAS –
    e.V.

  • How to Apply

    Prerequisites
    The course is aimed at research scientists with a minimum of a degree in
    a biological discipline, including laboratory and clinical staff, as well
    as specialists in related fields.

    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 £590 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
    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.