Biochemical Pathways and Large Scale Metabolic Networks

Welcome and introduction

Marco Pagni (Vital-IT group, SIB)

Public databases of metabolites, biochemical reactions and enzymes, web-based and programmatic accesses

Kristian Axelsen & Thierry Lombardot (both Swiss-Prot group, 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

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?

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)

Useful software for working with metabolic networks
 * Escher for visualization and reconstruction
 * KEGGtranslator
 practical exercise: reconstruction using online resource lookup

Hybrid Models of Metabolic Networks

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

Details:
- 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

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
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

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:
- 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

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

Orthology and Comparative Genomics

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

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