PhD project of Christopher Schölzel: Object-oriented multi-scale modeling of biological systems with Modelica using the example of the human cardiovascular system
Modelica is an object-oriented acausal modeling language built for complex cyberphysical systems including both continuous variables and discrete events. Models can be formulated in a purely declarative mathematical way or by graphically combining pre-built components in a diagram view.
In contrast to traditional approaches using languages like C and Matlab, the equations are arranged and solved entirely by a solver backend. This allows for a very consise hierarchical description that lends itself well to multi-scale modeling of biological systems.
In my thesis I investigate the usefulness of Modelica in systems biology by taking the example of the Seidel-Herzel model of the human cardiovascular system, which includes the function of baroreceptors, the lungs, the heart, and the autonomous nervous system.
Rhizoctonia solani is a species complex of pathogenic fungi that affects numerous economically important plants, causing enormous losses in agriculture. Isolates from the anastomosis group AG 1-IB affect lettuce (Lactuca sativa), causing seedling damping off and bottom rot.
The establishment of sequencing and annotation strategies for the fungus will be a powerful tool for the analysis of virulence determinants on group or subgroup level, for comparative genomics, population genetics as well as for the investigation of different life styles determined by genetic factors. An established genomic sequence will then allow transcriptomic analyses using microarrays, DNA-chips and RNA-Seq.