title: LBIBCell: a cell-based simulation environment for morphogenetic problems.
abstract: BACKGROUND
  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.
  
  
  METHODS
  The documentation and source code are available on http://tanakas.bitbucket.org/lbibcell/index.html
authors.affiliation: Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Simon
authors.initials: S
authors.lastname: Tanaka
authors.affiliation: Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and.
authors.forename: David
authors.initials: D
authors.lastname: Sichau
authors.affiliation: Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland and Swiss Institute of Bioinformatics, Basel, Switzerland.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Iber
mesh_terms: D000465:Algorithms; D002450:Cell Communication; D002454:Cell Differentiation; D002455:Cell Division; D003198:Computer Simulation; D004777:Environment; D045604:Extracellular Fluid / Q000737:chemistry*; D006801:Humans; D008962:Models, Theoretical; D009024:Morphogenesis / Q000502:physiology*; D012984:Software