Spatial modeling in cell biology at multiple levels

Abstract

Most modeling and simulation approaches applied in cell biology assume a homogeneous distribution of particles in space, although experimental studies reveal the importance of space to understand the dynamics of cells. There are already numerous spatial approaches focusing on the simulation of cells. Recently, they have been complemented by a set of spatial modeling languages whose operational semantics are tied partly to existing simulation algorithms. These modeling languages allow an explicit description of spatial phenomena, and facilitate analysis of the temporal spatial dynamics of cells by a clear separation between model, semantics, and simulator. With the supported level of abstraction, each of those offers a different perception of the spatial phenomena under study. In this paper, we give an overview of existing modeling formalisms and discuss some ways of combining approaches to tackle the problem the computational costs induced by spatial dynamics.