Methods in Computational Systems Biology

Research Strategy

The group focuses on methodological research for mathematical modeling of biological processes. We develop and evaluate numerical methods and provide software as a service for the scientific community. Our main project in this field is COPASI, a software package for creating, simulating, and analyzing models of biochemical reaction networks that are used by thousands of researchers worldwide. As a complement, we also provide simulator software for spatial kinetic models. Our areas of expertise are kinetic modeling with stochastic simulations and ODEs, spatial kinetic modeling using PDEs, optimization techniques including parameter estimation, and constraint-based modeling.

As a long-term project, we will continue the established collaboration with Ursula Kummer’s group and international partners on the software COPASI . In methodological research, we will put a focus on spatial modeling, where we will develop new simulation techniques (in collaboration with P. Bastian, IWR, Heidelberg University), provide software support for building mathematical models from biological information, and especially develop parameter estimation methods for spatial models based on imaging data. We will apply these techniques in collaboration with the groups of Holger Erfle and Vytaute Starkuviene (both BioQuant) to develop modeling approaches that support advanced 3D cell culture experimental technologies.