Section outline

  • Monday 29 August 2016

     

    10:00 - 10:15 Welcome and introduction
    Marco Pagni (Vital-IT group, SIB)
    10:15 - 12:30

    Public databases of metabolites, biochemical reactions and enzymes, web-based and programmatic accesses
    Kristian Axelsen & Thierry Lombardot (both Swiss-Prot, SIB, Geneva)

    Details:
    - Compounds and reactions as building blocks for metabolic networks
    - Compounds: names, isomers, tautomers, charges, structures
    - Reactions: balancing
    - Enzymes: gene-protein-reaction (GPR) relations
    12:30 – 13:45 Lunch
    13:45 – 15:45

    Exercises / hands-on

    - Using websites of selected metabolites and reactions databases

    - Simple programmatic access using python
    15:45 – 16:15 Coffee break
    16:15 - 17:15

    Biochemical Pathway Representations: Specific Requirements of Genome-Scale Metabolic Networks
    Sébastien Moretti (Vital-IT group, SIB, Lausanne)

    Details:
    - What is a metabolic network/model?
    - What are model requirements?
    - How to compare models?