Modelling and Simulation of Complex Biological Systems

The goal of this project is the design and implementation of a simulator that allows to simulate the model of a biological cell in all life processes including the cell cycle. In order to allow such different life processes (metabolism, gene regulation, signal transduction etc.) to be modeled and simulated in a unique model, a hybrid simulator is designed which integrates deterministic and stochastic simulation techniques. The spatial subdivision of the simulation volume allows not only the modelling of diffusion processes but also the distribution of the huge amount of simulation data onto several processors of a parallel computer. For handling the simulation data advanced parallel and distributed algorithms, databases, visualization techniques and optimization and inference methods are used. The simulator is designed to support researchers in the process of modelling cell-biological processes (metabolic inverse problem) and in the process of design and optimization of biological systems (metabolic engineering).

Publications

  • M. Schwehm (2001): 'Parallel Stochastic Simulation of Whole-Cell Models', Proc. 2nd Int. Conf Systems Biology (ICSB 2001), Omnipress, pp. 333-341

  • M. Schwehm, S. Heeß, E. Rheinbay, M. Schröder (2001): 'Metabolizer: A Java Simulation Environment for Whole-Cell Models', Proc. 2nd Int. Conf Systems Biology (ICSB 2001), Omnipress, p. 119 (poster abstract).

  • M. Schwehm, N. Gehlenborg, H. Post, A. Stein and K. Weber (2001): 'Parallel Simulation Engines for Whole-Cell Models', Proc. 2nd Int. Conf Systems Biology (ICSB 2001), Omnipress, pp. 120 (poster abstract).

  • M. Schwehm (2001): 'Fast Stochastic Simulation of Metabolic Networks', In: E. Wingender, R. Hofestädt & I. Liebich (Eds.): 'Proc. German Conf. Bioinformatics (GCB 2001), pp. 223-226 (poster abstract).




Ansprechpartner

Dr. Markus Schwehm, Tel.: (07071) 29-78978, schwehm@informatik.uni-tuebingen.de