This course type is computational

Proteomics Bioinformatics

16 - 21 July 2017Wellcome 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 2016 course

    “I really enjoyed the course. I feel that I learned a lot, and I feel
    confident with practising on most of the tools were talked about”
    “Best course I have been on. Heavy workload but lectures/tutorials were
    mostly delivered at the right speed with a few exceptions. Very well
    organised and wonderful surroundings.”
    “Overall, this course was great! Each of the topics were good and the
    speakers were phenomenal! The instructors were great! Well organized!”

    “I found the course very valuable and well organised, and will utilise
    much of the information provided here. I am looking forward to analysing
    my own data with the tools provided.”
    “I would highly recommend this course to anyone that wants to use
    proteomics and bioinformatics in the future! I’m glad that I was able to
    participate!”
    “Excellent course and useful for anyone carrying out proteomics
    bioinformatics. Also suitable for both biologists and
    bioinformaticians”.

  • 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

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

    Guest speakers
    Pedro Beltrao EMBL-EBI, UK
    Jyoti Choudhary
    Wellcome Trust Sanger Institute, UK

  • 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 £680 towards board and lodging for
    non-commercial applicants. Please contact us for the commercial fee.

    Additional limited bursaries are available (up to 50%
    of the course fee)
    and are awarded on merit. Please see the “Bursaries”
    tab for details.

    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

    Travel visas
    Please contact the
    event organiser if you require a letter to support a travel visa
    application. Note that letters will be provided to confirmed attendees.

    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 and information for general visitors and business
    visitors.

  • Cost / Bursaries

    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 £680 towards board and lodging for
    non-commercial applicants. Please contact us for the commercial fee.

    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.