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Large-Scale Parameter Studies of Cell-Based Models of Tissue Morphogenesis Using CompuCell3D or VirtualLeaf

  • Margriet M. Palm
  • Roeland M. H. MerksEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1189)

Abstract

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.

Key words

Cellular Potts model CompuCell3D VirtualLeaf Angiogenesis Cell-based model Parameter study Quantification 

Notes

Acknowledgments

We thank Harold Wolff for thoroughly testing the materials and methods discussed in this chapter. We thank the Indiana University and the Biocomplexity Institute for providing the CompuCell3D modeling environment and SARA for providing access to the National Compute Cluster LISA. This work was financed by the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research. The investigations were in part supported by the Division for Earth and Life Sciences (ALW) with financial aid from the Netherlands Organization for Scientific Research (NWO).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Centrum Wiskunde & Informatica (CWI)AmsterdamThe Netherlands
  2. 2.Netherlands Consortium for Systems Biology/Netherlands Institute for Systems Biology (NCSB-NISB)AmsterdamThe Netherlands
  3. 3.Mathematical Institute LeidenLeidenThe Netherlands

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