Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.

Details

Serval ID
serval:BIB_0E9ECBD6E606
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.
Journal
Methods in Molecular Biology
Author(s)
Daub J.T., Merks R.M.
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Publication state
Published
Issued date
2015
Volume
1214
Pages
67-127
Language
english
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.
Keywords
Cellular Potts model, Agent-based modeling, Tissue Simulation Toolkit, Angiogenesis, Cell-based model, Parameter study, Quantification, Glazier-Graner-Hogeweg model
Pubmed
Web of science
Create date
14/01/2015 21:20
Last modification date
20/08/2019 12:35
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