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Large-scale parameter studies of cell-based models of tissue morphogenesis using CompuCell3D or VirtualLeaf

Margriet M. Palm and Roeland M.H. Merks (2015). Large-scale parameter studies of cell-based models of tissue morphogenesis using CompuCell3D or VirtualLeaf. In: Nelson, C.M. (ed.), Tissue Morphogenesis. Methods in Molecular Biology, vol. 1189, pp. 301-322, Springer-Verlag Berlin Heidelberg

Computational, cell-based models, such as the cellular Potts model (CPM) have become a widely-used tool to study tissue formation. Most  cell-based models mimic the physical properties of cells and their  dynamic behavior, and generate images of the tissue that the cells form  due to their collective behavior. Due to these intuitive parameters and output, cell-based models are often evaluated visually and the parameters are fine-tuned by hand. To get better insight into how in a cell-based model the microscopic scale (e.g., cell behavior, secreted molecular signals, and cell-ECM interactions) determines the macroscopic scale, we need to generate morphospaces and perform parameter sweeps, involving large numbers of individual simulations. This chapter describes a protocol and presents a set of scripts for automatically setting up, running and evaluating large-scale parameter sweeps of cell-based models. We demonstrate the use of the protocol using a recent cellular Potts model of blood vessel formation model implemented in CompuCell3D. We show the versatility of the protocol by adapting it to an alternative cell-based modeling framework, VirtualLeaf. [ http://link.springer.com/protocol/10.1007%2F978-1-4939-1164-6_20#page-1 ]