4th Workshop on Computation of Biochemical Pathways
and Genetic Networks

Villa Bosch
Heidelberg
September 12-13, 2005

Program

Monday, 12th

08:30 - 09:00 Registration
09:00 - 09:15 Welcome and Organisatorial Issues

09:15 - 12:15 Session 1: Network Analysis

09:15 - 09:50 Modeling and Simulation of Large-scale Signal Transduction Networks (Roland Eils)
09:50 - 10:25 Link between Logical Structure and Dynamics: The Example of the p53-mdm2 Network (Marcelline Kaufman)
10:25 - 10:45 Coffee break
10:45 - 11:20 Domain-oriented and Modular Approaches to the Reduction of Mathematical Models of Signaling Networks (Julio Saez-Rodriguez)
11:20 - 11:55 Dimension Reduction by Balanced Truncation Applied to a Model of Glycolysis (Wolfram Liebermeister)
11:55 - 12:15 General discussion of the session

12:15-14:00 Lunch break

14:00 - 16:30 Session 2: Stochastic Methods

14:00 - 14:35 Bridging the Scales in Biochemical Simulation (Linda Petzold)
14:35 - 15:10 Particle-based Stochastic Simulations (Nicolas Le Novère)
15:10 - 15:45 Stochastic Models for Circadian Rhythms (Didier Gonze)
15:45 - 16:15 Coffee break
16:15 - 16:30 General discussion of the session

16:30 - 18:30 Poster presentation and mini-talks

19:00 Workshop dinner

Tuesday, 13th

09:00 - 12:00 Session 3: Tools

09:00 - 09:35 Trends in Bifurcation Software: From CONTENT to MATCONT (Yuri Kuznetsov)
09:35 - 10:10 Stimulus Response Experiments for Model Driven Discovery (Wolfgang Wiechert)
10:10 - 10:30 Coffee break
10:30 - 11:05 SABIO-RK - a Reaction Kinetics Database (Isabel Rojas)
11:05 - 11:40 BioModels.net, Tools and Resources to Support Computational Systems Biology (Nicolas Le Novère)
11:40 - 12:00 General discussion of session

12:00 - 14:00 Lunch break

14:00 - 17:00 Session 4: Reconstruction of Genetic Networks

14:00 - 14:35 Integrating Predicted Protein Localization with Protein-protein Interaction Data: The Human Nucleolus (Søren Brunak)
14:35 - 15:10 System Indentification of Biochemical Networks Using Discrete Models (Reinhard Laubenbacher)
15:10 - 15:30 Coffee break
15:30 - 16:05 Distribution of a Bifurcation Parameter in a Genetic Network with Uncertain Parameters (Edda Klipp)
16:05 - 16:40 Validation of Qualitative Models of Genetic Regulatory Networks by Model Checking (Gregory Batt)
16:40 - 17:00 General discussion of session

4th Workshop on Computation of Biochemical Pathways and Genetic Networks

Villa Bosch Heidelberg September 12-13, 2005