Simon Tanaka1, David Sichau2, Dagmar Iber1. 1. Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and Swiss Institute of Bioinformatics, Basel, Switzerland. 2. Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and.
Abstract
MOTIVATION: The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required. RESULTS: We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics. AVAILABILITY AND IMPLEMENTATION: The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html
MOTIVATION: The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events, such as cell division, cell-cell interactions and spatially restricted signalling events. A tightly coupled cell-based mechano-regulatory simulation tool is therefore required. RESULTS: We developed an open-source software framework for morphogenetic problems. The environment offers core functionalities for the tissue and signalling models. In addition, the software offers great flexibility to add custom extensions and biologically motivated processes. Cells are represented as highly resolved, massless elastic polygons; the viscous properties of the tissue are modelled by a Newtonian fluid. The Immersed Boundary method is used to model the interaction between the viscous and elastic properties of the cells, thus extending on the IBCell model. The fluid and signalling processes are solved using the Lattice Boltzmann method. As application examples we simulate signalling-dependent tissue dynamics. AVAILABILITY AND IMPLEMENTATION: The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html
Authors: Paul Van Liedekerke; Johannes Neitsch; Tim Johann; Enrico Warmt; Ismael Gonzàlez-Valverde; Stefan Hoehme; Steffen Grosser; Josef Kaes; Dirk Drasdo Journal: Biomech Model Mechanobiol Date: 2019-11-20
Authors: M E Johnson; A Chen; J R Faeder; P Henning; I I Moraru; M Meier-Schellersheim; R F Murphy; T Prüstel; J A Theriot; A M Uhrmacher Journal: Mol Biol Cell Date: 2020-11-25 Impact factor: 4.138
Authors: James M Osborne; Alexander G Fletcher; Joe M Pitt-Francis; Philip K Maini; David J Gavaghan Journal: PLoS Comput Biol Date: 2017-02-13 Impact factor: 4.475
Authors: Paul Van Liedekerke; Johannes Neitsch; Tim Johann; Kevin Alessandri; Pierre Nassoy; Dirk Drasdo Journal: PLoS Comput Biol Date: 2019-03-08 Impact factor: 4.475