Section outline

  • General

    Collapse all Expand all
    logo cuso

    Biochemical Pathways and Large Scale Metabolic Networks

    Lausanne, 29 August - 2 September 2016

    Location: Génopode Building, room 2020

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Technical / software prerequisites

    You need to bring a laptop with administrator rights (meaning you can install programs yourself) equipped with:

    - a recent browser version

    - SSH terminal with X session:

       * for Windows: MobaXterm (terminal for Window with X server included). Choose "Installer edition"

       * for Mac: a terminal is included but you need to have an X server. You can   install XQuartz

       for Linux: should be fine

    - Java 8 (at least Run Time Environment (JRE), see https://www.java.com, better the full JDK (Java Development Kit) to make sure everything will run).

    - A suitable editor for XML:

       * for Windows: http://www.winedt.com/ or http://www.heise.de/download/product/easy-xml-editor-39120/download or https://www.microsoft.com/en-us/download/details.aspx?id=7973

       * for Mac & Linux have some on board already

    The list below contains software that will be used during the practical. They will be accessible from a cluster server, but you can also install them locally if you want:

    - Python 2.7    (https://www.python.org/downloads/)
    - Java JRE (http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html)
    - COBRApy    (https://pypi.python.org/pypi/cobra)
    - suds-jurko    (https://pypi.python.org/pypi/suds-jurko)
    - lxml (https://pypi.python.org/pypi/lxml)

    - R        (https://cran.r-project.org/)
    - sybil        (http://cran.at.r-project.org/web/packages/sybil/)
    - glpkAPI    (http://cran.at.r-project.org/web/packages/glpkAPI/)
    - glpk        (https://www.gnu.org/software/glpk/) WinGLPK for Windows users (https://sourceforge.net/projects/winglpk/)
    - clpAPI    (http://cran.at.r-project.org/web/packages/clpAPI/)
    - COIN-OR (clp)    (http://www.coin-or.org/download/binary/CoinAll/)

    Optional:
    - RStudio    (https://www.rstudio.com/products/rstudio/download2/)

    Very optional:
    - Matlab

    If you have issues with installation, you can contact us

  • Topic 3

    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?

  • Topic 4

    Tuesday 30 August 2016

    09:00 - 10:30

    Introduction to online metabolic pathway databases
    Nathan E. Lewis (Systems biochemistry and cell engineering lab, University of California, San Diego) & Andreas Dräger (Systems Biology group, University of Tübingen)
    10:30 - 11:00 Coffee break
    11:00 - 12:30

    Exercises / hands-on
    Useful software for working with metabolic networks
     * Escher for visualization and reconstruction
     * KEGGtranslator
     practical exercise: reconstruction using online resource lookup
    12:30 – 13:45 Lunch
    13:45 – 15:45 Introduction to constraint-based modeling and Tutorial on COBRApy
    15:45 – 16:15 Coffee break
    16:15 - 17:15 Reconstruction and simulation of networks
    Practical exercise in metabolic engineering using COBRApy/COBRA Toolbox and visualizaion of results and data with Escher

  • Topic 5

    Wednesday 31 August 2016

    09:00 - 10:30

    Hybrid Models of Metabolic Networks
    Jörg Stelling (Computational Systems Biology Group, SIB & ETH Zurich D-BSSE, Basel)

    Details:
    1. FBA and its variants: Mathematical foundations, linear and non-linear optimization
    2. Incorporating experimental data: metabolic flux analysis, integration of -omics data
    3. Toward hybrid models: regulatory logig, dynamic FBA
    10:30 - 11:00 Coffee break
    11:00 – 12:30 Continued
    12:30 – 14:00 Lunch
    14:00 - 17:00

    Mini-Symposium

    14:00 - 14:40
    A hierarchy of decisions that impact the accuracy of tissue-specific metabolic models.
    Prof. Nathan E. Lewis
    Systems biochemistry and cell engineering lab, University of California, San Diego

    14:40 - 15:20
    Automated generation of realistic models.
    Prof. Dr. Jörg Stelling
    Computational Systems Biology Group, SIB & ETH Zurich D-BSSE, Basel

    15:20 - 15:40
    Break

    15:40 - 16:20
    Towards a more accurate prediction of the biotransformation of chemical contaminants - What can we learn from combining data mining, analytical chemistry and biology tools?
    Dr. Kathrin Fenner
    Department Environmental Chemistry, EAWAG, Dübendorf

    16:20 - 17:00
    Gene Ontology: biases, pitfalls, remedies.
    Prof. Christophe Dessimoz,
    Computational Evolutionary Biology and Genomics, SIB & Department of Ecology and Evolution, University of Lausanne

  • Topic 6

    Thursday 1 September 2016

    09:00 - 10:30

    EnviPath - database and prediction system for the microbial biotransformation of organic environmental contaminants
    Kathrin Fenner (Department Environmental Chemistry, EAWAG, Dübendorf) & Jörg Wicker (Data Mining Group, Johannes Gutenberg University, Mainz)

    Details:
    1. EnviPath database: environmental contaminants, elements of a pathway, databases, entering an own pathway, exercises;
    2. Pathway prediction: brainstorming rules, relative reasoning models, predicting pathways
    3. Advanced topics: technical about enviPath DB, interfaces (REST, API), batch processing, training on own relative reasoning model, exercises
    10:30 - 11:00 Coffee break
    11:00 - 12:30 Continued
    12:30 – 13:45 Lunch
    13:45 – 15:45

    The MetaNetX website for genome-scale metabolic network analysis and reconstruction. Usage of R software to analyze and exploit metabolic networks
    Marco Pagni, Van Du Tran, Sébastien Moretti (Vital-IT Center for high-performance computing of the SIB Swiss Institute of Bioinformatics, Lausanne)

    Details:
    1. Description and usage of MetaNetX
    1a. Automated Model Construction
    1b. Transfer of models


    2. Integration of transcriptomic data into genome scale metabolic networks:
    2a. Genome scale metabolic networks (GSMN): introduction, basic concepts, Sybil R package
    2b. Integrating transcriptomics into GSMN: gene expression with RNA-seq data, integration approaches for flux distribution prediction and context-specific GSMN construction
    2c. Exercises
    15:45 – 16:15 Coffee break
    16:15 - 17:15 Continued

  • Topic 7

    Friday 2 September 2016

    09:00 - 10:30

    Orthology and Comparative Genomics
    Christophe Dessimoz (Computational Evolutionary Biology and Genomics, SIB & University of Lausanne)

    Details:

    - Tree thinking and tree inference
    - Orthology & paralogy
    - Function propagation
    10:30 - 11:00 Coffee break
    11:00 - 12:30

    Practical

    - Retrieving and interpreting orthologs with OMA
    - Optional exercise: inferring phylogenetic trees
    12:30 – 13:45 Lunch
    13:45 – 16:00 Afternoon examination for those wanting ECTS credits