BioShape - a 3D Modelling and Simulator Environment for Biological Systems

BioShape [1, 2] is a uniform, particle-based, 3D space- and geometry-oriented multiscale modelling and simulation environment for the study of biological systems. It is particle-based because it treats any biological entity simply as a geometric shape able to perceive, interact and move in a space. It is uniform since the same shape-based representation can be exploited to model phenomena at very different temporal and spatial scales. BioShape is formally based on the Shape Calculus [3, 4], a bio-inspired timed and spatial calculus for describing 3D geometrical shapes moving in a space. Shape Calculus models act as a sort of simulation stub for BioShape: the simulated processes are formally defined as Shape Calculus process terms and then imported in the simulation, where they are enriched with many other modelling features such as personalized movements, perception, interactions with chemical gradients and so forth. To ease the import of Shape Calculus models in BioShape, the language has been refined [6] by adding a more detailed, finitary, geometric representation of shapes. The resulting language maintains the same characteristics of the original one adding a simple, yet powerful, way to define and manage geometries. BioShape is applied to the bone remodelling process, a typical micro-macro phenomenon that occurs in every living being with skeleton (see [5]). In a healthy individual, remodelling does not alter the global morphology/mass of the bone; on the contrary, in presence of Osteoporosis, Diabetes or other diseases, the equilibrium is broken, with high impact on the organism. BioShape simulations have the objective, with a strict collaboration with expert bioengineers/biologists, to improve the understanding of this biological process, from a qualitative and a quantitative point of view