Martin Falk - Visualization and Mesoscopic Simulation in Systems Biology

Speaker: Martin Falk, University of Stuttgart Visualisation Research Centre, Germany.

Time: Wed 15/8, 15:15-16:00

Place: VR-Arena, Visualization Center C


In systems biology, the characteristics and complex interactions of all elements in a particular biological system are investigated using quantitative methods from systems theory. In the presentation, a simplified cell model will be employed to study signal transduction pathways on a microscopic, cellular scale.

The process of model development is typically divided into four steps, namely modeling, evaluation, analysis, and refinement. These steps are detailed in the talk. By extending the Systems Biology Graphical Notation (SBGN) toward spatial cellular structures and interactions, a three-dimensional cell model can be defined. The model itself is evaluated on the GPU with a particle-based simulation. Several visualization approaches will be presented, visualizing the simulation results interactively in different ways. After defining the individual modeling steps, we tightly link them implementing a framework for model development. Finally, an outlook is given on how the presented methods can be applied to multiscale models such as drug administration affecting a tumor.