Cell-Based Computational Modeling of Vascular Morphogenesis Using Tissue Simulation Toolkit

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1214)

Abstract

Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis. However, experimenting with published simulation models or adding new assumptions to those models can be daunting for novice and even for experienced computational scientists. Here, we present a step-by-step, practical tutorial for building cell-based simulations of vascular morphogenesis using the Tissue Simulation Toolkit (TST). The TST is a freely available, open-source C++ library for developing simulations with the two-dimensional cellular Potts model, a stochastic, agent-based framework to simulate collective cell behavior. We will show the basic use of the TST to simulate and experiment with published simulations of vascular network formation. Then, we will present step-by-step instructions and explanations for building a recent simulation model of tumor angiogenesis. Demonstrated mechanisms include cell–cell adhesion, chemotaxis, cell elongation, haptotaxis, and haptokinesis.

Key words

Cellular Potts model Agent-based modeling Tissue Simulation Toolkit Angiogenesis Cell-based model Parameter study Quantification Glazier-Graner-Hogeweg model 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
  2. 2.Swiss Institute of BioinformaticsLausanneSwitzerland
  3. 3.Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
  4. 4.Centrum Wiskunde & InformaticaAmsterdamThe Netherlands
  5. 5.Mathematical InstituteUniversity LeidenLeidenThe Netherlands

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