Methods in Computational Systems Biology
Dr. Sven Sahle
We specialize in methodological research for mathematical modeling in biology. We create and assess numerical methods, offering software as a resource for the scientific community. Our primary project, COPASI, aids in creating, simulating, and analyzing biochemical reaction network models, widely adopted by researchers. We also provide spatial kinetic model simulation software, excelling in stochastic simulations, ODEs, PDE-based spatial modeling, optimization methods, and constraint-based modeling.
Research Strategy
Our main project in this field is COPASI, a software package for creating, simulating and analyzing models of biochemical reaction networks that is used by thousands of researchers worldwide. As a complement, we also provide a 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.
Dr. Sven Sahle
+49 (0)6221 54-51272
sven.sahle@bioquant.uni-heidelberg.de
BioQuant, Im Neuenheimer Feld 267
Future Direction
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 Peter 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 a collaboration with the BioQuant working groups of Holger Erfle and Vytaute Starkuviene to develop modeling approaches that support advanced 3D cell culture experimental technologies.