LBIBCell: a cell-based simulation environment for morphogenetic problems

Bioinformatics
Simon TanakaDagmar Iber

Abstract

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. 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. The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html

References

Dec 7, 1979·Journal of Theoretical Biology·J Schnakenberg
Dec 1, 1972·Kybernetik·A Gierer, H Meinhardt
May 20, 1998·Biophysical Journal·G ForgacsM S Steinberg
Sep 28, 1992·Physical Review Letters·F Graner, J A Glazier
Feb 12, 2004·Bulletin of Mathematical Biology·Katarzyna A RejniakLisa J Fauci
Feb 9, 2005·Physical Review Letters·Yeh-Shiu ChuFrederic Pincet
Dec 18, 2007·Current Biology : CB·Reza FarhadifarFrank Jülicher
Jul 1, 2005·Mathematical Biosciences and Engineering : MBE·T J Newman
Aug 17, 2010·Bioinformatics·Stefan Hoehme, Dirk Drasdo
Dec 15, 2010·Plant Physiology·Roeland M H MerksGerrit T S Beemster
Feb 8, 2011·Cell·Nicolas MincFred Chang
Feb 24, 2012·PLoS Computational Biology·Denis MenshykauDagmar Iber
Apr 10, 2012·Methods in Cell Biology·Maciej H SwatJames A Glazier
Sep 4, 2012·Journal of Theoretical Biology·Shuji Ishihara, Kaoru Sugimura
Dec 20, 2012·Scientific Reports·Amarendra BaduguDagmar Iber
Mar 22, 2014·Current Biology : CB·Simon RestrepoKonrad Basler

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Citations

Feb 14, 2017·PLoS Computational Biology·James M OsborneDavid J Gavaghan
Nov 12, 2019·Physical Biology·Anna StopkaDagmar Iber
Nov 22, 2019·Biomechanics and Modeling in Mechanobiology·Paul Van LiedekerkeDirk Drasdo
Jun 25, 2020·PLoS Computational Biology·Jakob RosenbauerAlexander Schug
Oct 30, 2015·Briefings in Bioinformatics·Dagmar IberErkan Ünal
Mar 31, 2019·Bulletin of Mathematical Biology·Henri B WolffRoeland M H Merks
Mar 30, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alexander G FletcherRuth E Baker
Aug 28, 2020·Molecular Systems Biology·Sarah M KeatingUNKNOWN SBML Level 3 Community members

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