Pathways, Networks and Systems

Downloadable poster in PDF

   IMPORTANT DATES for this Course
   Deadline for applications: October 7th 2013
   Notification of acceptance within 72 hours of application (working days count)
   Course date: October 15th to October 17th 2013


Christoph Wierling studied Biology at the University of Münster and obtained a PhD in biochemistry at the Free University of Berlin. His research interest focuses on modeling and simulation of biological systems and the development of systems biology software. Currently he works as a group leader of the systems biology group at the Max Planck Institute for Molecular Genetics in Berlin. He participated in PA09 and PA11 Pathway Analysis courses of GTPB as an instructor and in PathProt-II as a speaker.

Max Plank Institute, Berlin, DE

Alexander Kel is the Founder and Chief Scientific Officer (CSO) of geneXplain GmbH. He has been involved in research in practically all fields of bioinformatics, from molecular evolution, and structural biology to database development, application of machine learning techniques and sequence analysis. In the recent years his interests shifted considerably towards system biology including structural analysis of signal transduction and gene regulatory pathways and dynamic modelling of regulatory circuits of such complex cellular processes as cell cycle, differentiation and apoptosis. He participated in all the Pathway Analysis and in all the Hunting for Genes and Promoters courses of GTPB as an instructor. He is a co-founder of PathProt together with Roman Zubarev and Pedro Fernandes.

genExplain GmbH, Wolfenbuettel, DE

Olga Kel-Margoulis Having a very strong background in life sciences, Olga has acquired a rich experience with a broad range of bioinformatics applications. In particular, she is an expert in all aspects of database curation as well as in biological interpretation of microarray data. At her previous position, Olga was responsible for organizing the curation process of the TRANSFAC and TRANSPATH databases.

genExplain GmbH, Wolfenbuettel, DE

Course description:

Recent technological advances in high-throughput methods (such as NGS) and quantitative proteomics, allow us to analyse each individual all the way down to his/her proteins and chemicals and his/her own DNA sequences in just a few hours. In near future we may expect that a specifically trained physician will be able to use this type of data and quickly find support for deciding on individualised therapy, on the basis of analyses made on these data: which drugs, what health risks, what consequences of lifestyle changes, which diets or rehabilitation measures are appropriate for a patient with such an individualised profile.

This training course we will provide hands-on experience on the analysis and modeling of biological systems from several angles. First of all, we will introduce systems biology and modeling from an interaction- and network-based perspective. We will familiarise the audience with publicly available data resources, pathways databases, Reactome, KEGG, TRANSPATH, TRANSFAC and ConsensusPathDB. Next, we will provide a soft introduction to mathematical modeling of biological systems, and we will look at different mathematical modeling stategies using simple Boolean networks, Petri Nets and ordinary differential equation systems (ODEs). We will train the participants in the use of computational tools, such as Cytoscape and CellDesigner, for the set-up and development of model prototypes. We will then move into the usage of Copasi, BioUML and PyBioS, that can handle parameter-fitting and sensitivity analysis.

We will then look at methods for reconstructing gene regulatory networks from gene expression data. It will introduce methods of analysis of topological properties of biochemical and regulatory networks. This will lead us to the application of such methods to revealing key nodes in networks as potential biomarkers or drug targets. The participants will be developing group work towards the validation of such drug targets, with the help of dynamic modeling of the network systems. We will work with real case examples of application of these methods for identification of disease related biomarkers, drug discovery and personalized medicine. In some of our hands-on training sessions we will be constructing workflows "From genome to drug targets" using the flexible geneXplain platform.

Target Audience

The course is has been designed for a variety of recepients. It starts from scratch in many aspects, thus the low level of prerequisites. The participants can expect to enter the area of modelling and analysis using systems level tools via a smooth introduction, built from simple concepts. On the third day they will be sufficiently equipped to understand how address biological problems (such as regulation) with a biological networks approach, and take it to practice using open source software whenever possible. The course will be great for those who want to address tailored, targeted and personalised medicine, for example. But it will also be of instrumental usefulness to those who want to understand signalling and regulation themselves. Finally, it will also be an easy way in for those who are interested in understanding the practicalities of interfering with biological systems, identifying pathways, knocking them down, repairing them, etc.

Course Pre-requisites

Basic computing skills, graduate level in Life Sciences, intermediate level in Biostatistics.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  September 21st 2013