Systems Biology at the Center for BioSystemsAnalysis ZBSA

„To understand complex biological systems requires the integration of experimental and computational research -- in other words a systems biology approach“ Hiroaki Kitano, Nature 2002 "Systems biology...is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programmes, but different....It means changing our philosophy, in the full sense of the term“ Denis Nobel, 2006 Systems Biology

NEW KNOWLEDGE EXPERIMENTAL DATA; KNOWLEDGE OF STRUCTURES; FUNCTIONS AND INTERACTIONS MATHEMATICAL MODEL BIOLOGICAL PHENOMENON IN VITRO-/ IN VIVO- EXPERIMENT IN SILICO EXPERIMENT (SIMULATION) NEW DATA HYPOTHESIS

Life Sciences, Engineering, Computer Sciences and Mathematics merge at the ZBSA NATURE|Vol 445|22 February 2007

ZBSA Prof. Jens Timmer Acting Director Prof. Ralf Baumeister Founding Director ( ) Prof. Wolfgang Driever Initiator ( ) Director since 7/2010

Scientists from six faculties work together in multidisziplinary projects at the ZBSA Medicine Mathematic s Physics Biology Chemistry Pharmacology Forestry and Environment Informatics and Microsystems Bernstein Center for Computational Neuroscience

Structure of the ZBSA Structure ZBSA Bioinformatics – Data Management Systems Biology -Modelling Core Facilities – Measurement Technology Metabolomics Life Imaging ProteomicsGenomics Data Acquisition Data Analysis Scientific Focus Metabolic Networks Regulatory Networks: Supracellular Molecular Systems Cellular Systems Project Areas Structure ZBSA Bioinformatics – Data Management Systems Biology -Modelling Core Facilities – Measurement Technology Metabolomics Life Imaging ProteomicsGenomics Data Acquisition Data Analysis Scientific Focus Metabolic Networks Regulatory Networks: Supracellular Molecular Systems Cellular Systems Project Areas Bioinformatics – Data Management Systems Biology -Modelling Core Facilities – Measurement Technology Metabolomics Life Imaging ProteomicsGenomics Data Acquisition Data Analysis Scientific Focus Metabolic Networks Regulatory Networks: Supracellular Molecular Systems Cellular Systems Project Areas

Genetic dispositionDevelopment Environment Proteins, Protein- Networks Genes, Gene Networks Metabolites, metabobic Neworks Systems Biology Metabolomics Genomics Proteomics Life Imaging

ZBSA – an Interdisciplinary Center Technologies Genomics Proteomics Imaging Metabolomics Seminars and MeetingsJunior Groups IT and Theory Data Analysis Modelling Land Baden-Württemberg: Building: 17,5 Mio Euro Equipement: 2,5 Mio Euro

Core Facilities for Quantitative High Quality Data: The Experimental Basis for Modelling and Systems Analysis MetabolomicsGenomicsProteomicsLife Imaging Dr. Kurz Dr. Schlosser Dr. Kammerer Dr. Nitschke

The ZBSA is instrumental for the excellence research centers at the University of Freiburg Research Cluster of Excellence FRIAS LiFENET Freiburg Institute of Advanced Studies Complex systems – systems biology Graduate School

The Freiburg Initiative for Systems Biology - FRISYS  Integration of theoretical and experimental efforts to define intact biological systems  Modelling and systems’ analysis of signalling processes in growth and differentiation  Model organisms at phylogenetic key positions  Dedicated Systems Biology curriculum in order to train highly qualified scientists for this field Coordinator: Wolfgang R. Hess

AKT1 Systembiologie des Alterns InsR PI3K PIP3 PTEN PIP2 PDK1 AKT2 SGK1 FOXO ? MAPKKK MAPKK MAPK SKN-1 SKN1 EGFR RAF GRB-2 RAS stress developmental +neuronal signals stress, insulin nutrients + ? JNK JKK ? SHC-1 cell cycle control apoptosis stress response ageing stress response ageing, telomere maintenance SOS MEK MAPK SIR2 PEPT1 Raptor TOR ? eIF4B S6K ? cellular senescence protein integrity stress control DJ1 PINK1 ? Parkin? Proteomics Jörn Dengjel FRIAS LIFENET Signalling Tilmann Brummer bioss Networks Enrico Schmidt FRISYS/bioss Modelling Hauke Busch FRIAS LIFENET Robotics and Automation Anke Becker FRISYS Promotion of Junior Faculty 14 Junior Faculty at ZBSA

Research – Strategic Areas Systems biology of development and differentiation Signaling and decision mechanisms in cell populations Dynamic control of cell states by transcriptional networks and regulatory RNAs

Research – Future plans Collaborative Research Center CRC of German Research Council DFG Quantitative analysis and modelling of mechanisms in development and differentiation Trinational initiative of Freiburg with –IGBMC Strasbourg –BSSE / ETH at Basel

Legend: EUCOR University Strasbourg SystemsX Basel/Zurich Systems Biology In the D – F – CH Trinational region International Network

Where are all the ZBSA Systems Biologists?

2nd Annual ZBSA Retreat Feldberg-Altglasshütten November

Thank you for your attention! Wolfgang Driever

Systems Biology "Systems Biology aims at an improved understanding of biology and its mechanisms, in particular of the functions and interactions of key elements of living systems (DNA, RNA, proteins, cells). Systems biology is the sum of novel methodological approaches to (a) gather and analyse this knowledge, (b) to translate this knowledge into a thorough understanding that eventually will allow predicting the behavior of the complex and dynamic networks that regulate living specimen. The focus of systems biology is clearly not limited to the description of existing knowledge using a different syntax, but aims at combining available methods synergistically to develop novel approaches for the characterization of the behavior of biological networks. Whereas traditional research in the Life Sciences generally emphasizes the operational necessity of a gene, protein, component for the correct execution of a particular pathway or regulatory mechanism (what is it doing, is it necessary or sufficient?), it is the Systems Biology that expands these questions in an attempt to define the relevance of a particular component or mechanism for fulfilling a biological goal (Why is it performing the way it is to accomplish this or that task? How does the component need to be designed in order to fulfill its function)." Prof. Ralf Baumeister Director ZBSA