The simulation and visualization of biological system models is becoming more and more important both in clinical use and in basic research. Since many systems are characterized by interactions involving different scales at the same time, several approaches have been defined to handle such complex systems at different spatial and temporal scale. In this context, we propose BioShape, a 3D particle-based spatial simulator whose novelty\ud consists of providing a uniform and geometry-oriented multiscale modeling environment.\ud These features make BioShape "scale-independent'', able to\ud express geometric and positional information, and able to support transformations between scales simply defined as mappings between different granularity model instances. To highlight BioShape peculiarities, we sketch a multiscale model of human aortic valve where shapes are used at the cell scale for describing\ud the interaction between a single valvular interstitial cell and its surrounding matrix, at the tissue scale for modeling the valve leaflet tissue mechanical behaviour, and at the organ scale for reproducing, as a 3D structure with fluid-structure interaction, the\ud motion of the valve, blood, and surrounding tissue

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In this paper we study the liveness of several MUTEX solutions by representing them as processes in PAFAS s, a CCS-like process algebra with a specific operator for modelling non-blocking reading behaviours. Verification is carried out using the tool FASE, exploiting a correspondence between violations of the liveness property and a special kind of cycles (called catastrophic cycles) in some transition system. We also compare our approach with others in the literature. The aim of this paper is twofold: on the one hand, we want to demonstrate the applicability of FASE to some concrete, meaningful examples; on the other hand, we want to study the impact of introducing non-blocking behaviours in modelling concurrent systems

Many biological phenomena are inherently multiscale, i.e. they are characterised by interactions involving different scales at the same time. This is the case of bone remodelling, where macroscopic behaviour (at organ and tissue scale) and microstructure (at cell scale) strongly influence each other. Consequently, several approaches have been defined to model such a process at different spatial and temporal levels and, in particular, in terms of continuum properties, abstracting in this way from a realistic - and more complex - cellular scenario. While a large amount of information is available to validate such models separately, more work is needed to integrate all levels fully in a faithful multiscale model.\ud \ud In this scenario, we propose the use of BioShape, a 3D particle-based, scale-independent, geometry and space oriented simulator. It is used to define and integrate a cell and tissue scale model for bone remodelling in terms of shapes equipped with perception, interaction and movement capabilities. Their in-silico simulation allows for tuning continuum-based tissutal and cellular models, as well as for better understanding - both in qualitative and in quantitative terms - the blurry synergy between mechanical and metabolic factors triggering bone remodelling

The Shape Calculus is a bio-inspired timed and spatial calculus for describing 3D geometrical shapes moving in a space. Shapes, combined with a behaviour, form 3D processes, i.e., individual entities able to bind with other processes on compatible spatial channels and to split over previously established bonds. Due to geometrical space, timed behaviours, a wide degree of freedom in defining motion laws and usual nondeterminism, 3D processes typically exhibits an infinite behaviour that prevents any decidable analysis. Shape Calculus models are currently used only for simulation and, thus, validation of models and hypothesis testing. In this work we introduce a complementary, and synergetic, way of using the calculus for systems biology purposes: we define a first abstract interpretation that can be used to verify untimed and unspatial safety properties of a given model. Such an abstraction focuses on the possible interactions that, during the evolution of the system, can occur among processes yielding new composed processes and, thus, new species. Other possible abstract domains for the verification of more expressive properties are also discussed