Space, Geometry, Motion and Interactions in Modeling Biological Systems: the BioShape Approach

We present BioShape, a modeling and simulation environment for biological systems at different scales. The basic assumption is that the system is modeled using autonomous entities that have a physical shape, move in a geometrical 3D space and can interact in different ways. The modeled biological phenomenon will be observed and analyzed as the emerging behavior of the entities' behaviors in the in-silico experiment (simulation) that is set up. We show several application areas of our approach at different levels: molecular, cellular and tissue. Moreover, we show that different levels can be specified uniformly within BioShape, making it a powerful multiscale environment.