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Arne T Bittig and Adelinde M Uhrmacher (2010)

Spatial Modeling in Cell Biology at Multiple Levels

In: Proceedings of the 2010 Winter Simulation Conference, ed. by B. Johansson, S. Jain, J. Montoya-Torres, J. Hugan, and E. Yücesan, pp. 608-619, IEEE.

Most modeling and simulation approaches applied in cell biology assume a homogeneous distribution of particles in space, although new experimental studies reveal the importance of space to understand the dynamics of cells. The reason for this is not the lack of approaches including space. However, those have previously been focused 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. Due to the computational costs induced by spatial dynamics, combining different levels appears a fruitful avenue of research and the natural next steps to take.

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