Topic outline

  • General

    SIB Protein Bioinformatics course

    Protein analysis using SIB web-based tools

    Lausanne, 18-22 March 2013

    Course description:

    Participants will learn how to work with proteins using web based tools from the SIB.
    The daily schedule generally consists of:

    • Two presentations
      An introductory talk by a SIB group leader followed by a more in depth, technical talk by a senior bioinformatician.
    • Practical exercises
      Supervised by members of the groups developing these software and databases.

    Requirements:

    Participants should bring a laptop with wireless connectivity and make sure they have the permission to install software if necessary.
    Knowledge of UNIX is NOT necessary.

    Registration:

    Registration is closed.

    The cost is

    • 300 CHF for SIB and academic members
    • 600 CHF for all other participants


    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    Do not hesitate to contact us if you have any question related to this course.

  • Monday March 18th

    Using sequence centered resources through the web and some of the tools used for annotation in these sequence centered resources.

    09:00
    Welcome
    Marc Robinson-Rechavi, group leader, Evolutionary Bioinformatics
    9:15
    ExPASy - SIB Bioinformatics Resource Portal
    Heinz Stockinger,
    Vital-IT
    Elisabeth Gasteiger,
    Swiss-Prot
    10:00
    Presentation of the SIB Swiss Institute of Bioinformatics
    Ron Appel, SIB Executive director
    10:20
    Coffee break
    10:45
    The Universal Protein Resource (UniProt)
    Marie-Claude Blatter, Swiss-Prot
    12:45
    Lunch break
    14:00
    Practicals - ExPASy Bioinformatics Resource Portal
    Swiss-prot and Vital-IT groups
    15:00
    Coffee break
    15:30
    Practicals - UniProt
    Swiss-prot and Vital-IT groups
  • Tuesday March 19th

    Using sequence centered resources through the web and some of the tools used for annotation in these sequence centered resources.

    09:00
    Standardization resources
    Pascale Gaudet, CALIPHO
    Alan Bridge, Swiss-Prot
    10:30
    Coffee break
    11:00
    PROSITE-HAMAP-automatic annotation
    Alan Bridge, Swiss-Prot
    13:00
    Lunch break
    14:00
    Practicals - PROSITE-HAMAP-automatic annotation
    Swiss-Prot and Vital-IT groups
    15:00
    Coffee break
    15:30
    neXtprot - exploring the universe of human proteins
    Amos Bairoch, group leader, CALIPHO
    Pascale Gaudet, CALIPHO
    16:30
    Practicals - neXtprot
    CALIPHO and Vital-IT groups
    19:30
    Social dinner!
  • Wednesday March 20th

    Protein structure: Going 3D!

    09:00
    SWISS-MODEL
    Torsten Schwede, group leader, Computational Structural Biology
    10:30
    Coffee break
    11:00
    Protein structure visualization and analysis with Swiss-PdbViewer - DeepView
    Nicolas Guex, Vital-IT
    12:30
    Lunch break
    14:00
    Practicals - SWISS-MODEL
    Computational Structural Biology group
    15:00
    Coffee break
    15:30
    Practicals - SWISS-MODEL next generation
    Computational Structural Biology group

    • As discussed during the practicals, you are welcome to send in advance the questions/sequences you would like to work with on Friday to the SWISS-MODEL team

  • Thursday March 21th

    Protein structure: Going 3D!

    09:00
    SwissDrugDesign
    Vincent Zoete, Associate Group Leader, Molecular Modelling Group
    10:00
    Coffee break
    10:30
    SwissDrugDesign (cont.)
    Vincent Zoete, Associate Group Leader, Molecular Modelling Group
    11:30
    Lunch break
    13:20
    Application of drug design to cancer therapy
    Olivier Michielin, group leader, Molecular Modelling Group
    14:00
    break
    14:30
    Practicals - SwissDock
    Molecular Modelling
    16:00
    Coffee break
    16:30
    Practicals - SwissBioisostere
    Molecular Modelling

  • Friday March 22nd

    Protein-Protein Interactions.

    09:00
    STRING
    Christian von Mering, group leader, Bioinformatics Systems Biology
    10:30
    Coffee break
    11:00
    Practicals - STRING
    Bioinformatics Systems Biology and Vital-IT groups
    12:30
    Lunch break
    13:30
    Practicals - Work on your protein!

    support from:
    Bioinformatics Systems Biology
    CALIPHO
    Computational Structural Biology
    Molecular Modelling
    Swiss-prot
    Vital-IT
    15:00
    Coffee break
    15:30
    Practicals - Work on your protein!

    support from:
    Bioinformatics Systems Biology
    CALIPHO
    Computational Structural Biology
    Molecular Modelling
    Swiss-prot
    Vital-IT