Topic outline

  • General

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    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

      • 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?

        • 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

          • 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

            • 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

              • 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