Topic 6

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

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