Hybrid Modelling and Process Optimization of Biological Systems

An environment has been developed which comprises mathematical methods, concepts, and tools to enable the processing of experimental data to usable new insights about biological systems. Therefore, a mathematical modelling concept - Hybrid Petri-Nets for biological applications (HPNbio) – has been defined which is properly adapted to the demands of biological process. This concept has been implemented with the object-oriented modelling language Modelica. The developed Modelica library, called PNlib (Petri Net library), in combination with an appropriate Modelica-tool enables graphical hierarchical modelling, hybrid simulation, and animation of HPNbio-models. Thereby, an additional Modelica library, called PNproBio (Petri Nets for process modelling of Biological systems), provides wrapped HPNbio which offers on the one hand an easy-use-model at the top level with an intuitive and familiar adapted biological view and on the other hand the flexibility and generality of the HPNbio concept at a lower level. Based on an established model, the underlying processes can be optimized. This process optimization procedure is performed by means of hybrid optimization methods, i.e. a global method is combined with a local method by use of a specific switching strategy, in order to realize an open-loop control for biological processes.