Biochemical Pathways and Large Scale Metabolic Networks

Date 29 August - 2 September 2016
Speaker(s) Marco Pagni and others
Cancellation deadline 18 Aug 2016
City Lausanne

This course is co-organised by the CUSO/StarOmics doctoral program. Priority is given to its members, but is open to everyone.


This course and mini-symposium aim at guiding the participants in the complexities of biochemical pathway reconstruction with some emphasis on genome-scale metabolic networks.

  • The course consists of selected chapters, which altogether will help the participants to integrate concepts, various data types and different software tools.
  • A few practical session will be organised to demonstrate how to build metabolic models and to produce valuable biological knowledge.
  • The aim of the mini-symposium is to highlight the current state of research in the field.



This course is open to everyone, but it is an advanced course with a broad scope and hence primarily aimed to PhD students or Postdocs in Biology or Bioinformatics with interest for Systems biology.


Learning objectives

At the end of the course, participants should have a good knowledge or understanding of:

  • the current state and the future direction of R&D in the field
  • some major public resources (web sites, databases)
  • algorithms specific to this field and some of their implementation



Knowledge / skills:
People are encouraged to come with their own problem (e.g. their favourite microbes genome or metabolic model). Programming skills (e.g. UNIX, see our tutorial), basic experience with R and knowledge in Biochemistry are recommended.

Bring a laptop. Specific software installation might be given later if needed.



Click here to register

Deadline for application and cancellation is set to the 15th of AugustCancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.



University of Lausanne / Genopode building, classroom 2020 (Metro M1 line, Sorge station)


Additional information

For administrative questions, please contact
For technical and scientific questions, please contact



Monday 29 August

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 group, SIB, Geneva)

- 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 break
13:45 - 15:45 Exercises / hands-on
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)

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


Tuesday 30 August

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

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 break
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

09:00 - 10:30

Hybrid Models of Metabolic Networks

Jörg Stelling (Computational Systems Biology Group, SIB & ETH Zurich D-BSSE, Basel)

- FBA and its variants: Mathematical foundations, linear and non-linear optimization
- Incorporating experimental data: metabolic flux analysis, integration of -omics data
- Toward hybrid models: regulatory logig, dynamic FBA

10:30 - 11:00 Coffee break
11:00 - 12:30 Continued
12-30 - 14:00 Lunch break
14:00 - 17:00

Mini-Symposium (free entrance)

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

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

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)
- EnviPath database: environmental contaminants, elements of a pathway, databases, entering an own pathway, exercises;
- Pathway prediction: brainstorming rules, relative reasoning models, predicting pathways
- 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 break
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)

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

09:00 - 10:30

Orthology and Comparative Genomics

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

1. Tree thinking and tree inference
2. Orthology & paralogy
3. Function propagation

10:30 - 11:00 Coffee break
11:00 - 12:30 Orthology and Comparative Genomics - practical
- retrieving and interpreting orthologs with OMA
- optional exercise: inferring phylogenetic trees
12:30 - 13:45 Lunch break
13:45 - 16:00 Afternoon examination for those wanting ECTS credits