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
        • 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