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

Détails

ID Serval
serval:BIB_0E9ECBD6E606
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.
Périodique
Methods in Molecular Biology
Auteur(s)
Daub J.T., Merks R.M.
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Statut éditorial
Publié
Date de publication
2015
Volume
1214
Pages
67-127
Langue
anglais
Résumé
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.
Mots-clé
Cellular Potts model, Agent-based modeling, Tissue Simulation Toolkit, Angiogenesis, Cell-based model, Parameter study, Quantification, Glazier-Graner-Hogeweg model
Pubmed
Web of science
Création de la notice
14/01/2015 22:20
Dernière modification de la notice
20/08/2019 13:35
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