Molecular networks in Toxicogenomics

Date: 21 - 23 May 2014
Venue: Max Planck Institute for Molecular Genetics (MPIMG)
Ihnestraße 63-73, 14195 Berlin, Germany
Visitor’s information:
Registration opens: 4th April 2014
Registration deadline: 13th May 2014
Participation: First come, first served


Course overview

Toxicogenomics aims at the prediction of toxicity endpoints of chemical compounds with high-throughput data. Bioinformatics and systems biology tools are indispensable for understanding the complex mechanisms induced by the chemicals. In this course we will introduce the diXa warehouse, an integrated system for chemical safety. A particular focus of diXa lies on the in-depth analysis of molecular networks, the drivers of biological function. In the course we will learn about experimental techniques for detecting these molecular networks and on-line resources for retrieving and analysing molecular interactions. Furthermore, mathematical tools for in silico analysis and modelling of chemical response will be taught. The course has a balanced mixture of lectures and hands-on sessions.


The course is intended for people who are interested in bioinformatics, network analysis and systems biology and their applications in toxicogenomics, in particular mechanistic analysis of chemical response. In addition, researchers working with toxicogenomics data learn state-of-the-art tools and resources for network analysis. It is expected that people have ground level experience in data analysis and toxicogenomics.

Syllabus, Tools and Resources

During this course you will learn about:

  • Microarray data analysis
  • Network module algorithms
  • Literature mining
  • Computational modelling
  • Working with graphs and networks with Cytoscape
  • ConsensusPathDB interaction resource
  • diXa warehouse for chemical safety

Learning Objectives

After this course you should be able to: 

  • access and work with the diXa warehouse
  • access and work with the ConsensusPathDB
  • generate and analyse networks with Cytoscape
  • understand the concepts of literature mining and network module identification
  • derive predictive networks from toxicogenomics data


Course material

Day 1 - 21st May 2014
10:00 - 10:30       Welcome & Registration (refreshments available)           
10:30 - 11:00       Introduction to the diXa project                (Vera Matser, EMBL-EBI)
11:00 - 12:00       diXa data warehouse (Ugis Sarkans, EMBL-EBI) 
12:00 - 13:00       Lunch   
13:00 - 14:30       Exploration of future development of diXa data warehouse (Vera Matser, EMBL-EBI)    
14:30 - 15:00       Coffee & tea break        
15:00 - 16:30       Exploration of future development of diXa data warehouse       
16:30                     Close of Day 1   

Day 2 - 22nd May 2014
09:00 - 09:30       Introduction to Networks and Pathways              
09:30 - 10:30       Molecular interaction networks               
                                (Uli Stelzl, Otto-Warbug-Laboratory, MPIMG)
10:30 - 11:30       Identification of predictive network modules – a comparative study       
                                (Moritz Beber, Dep. Vertebrate Genomics, MPIMG)
11:30 - 12:00       Coffee & tea break        
12:00 - 13:00       Network-based interpretation of toxicogenomics data 
                                (Ralf Herwig, Dep. Vertebrate Genomics, MPIMG)
13:00 - 13:30       Lunch   
13:30 - 14:30       Computational modelling of drug response        
                                (Christoph Wierling, Dep. Vertebrate Genomics, MPIMG)
14:30 - 15:30       ConsensusPathDB, practical session (1)
15:30 - 16:00       Coffee & tea break        
16:00 - 17:30       ConsensusPathDB, practical session (2)
17.30                     Close of Day 2   
19.00                     Dinner (optional)
Day 3 - 23rd May 2014
09:00 - 09:45       Hepatotoxicity-specific network and pathway development                      
                                (Dennie Hebels, Maastricht University)
09:45 – 10:30      Pathway robustness      
                                (Marcelo Segura, Imperial College London)
10:30 - 11:00       Coffee & tea break        
11:00 - 12:00       Literature mining            
12:00 - 12:30       Lunch   
12:30 - 14:00       Network analysis using Cytoscape, practical session        
14:00                     End of the course        


Registration for this course is now closed.

Please note that the registration fee of £110 includes:

  • Lunch, and refreshment breaks
  • Course materials
  • Use of a computer in the MPIMG IT Training Room throughout the course

There is an optional workshop dinner on 22nd May 2014 charged at £28

There will be a maximum of 20 - 25 participants on this course and registration is on a first-come, first-served basis

Please note that members of the EMBL-EBI Industry Programme will have their registration fee paid by the Industry Programme. One Nucleus members receive a 40% discount on the registration fee.

For more information or questions please contact