Computational Methods
We develop computational methods for the modeling and simulation of signalling networks, cell-based tissue simulations, image processing and image-based modelling.
Cell-based Tissue Simulation Framework
We have developed LBIBCell, PolyHoop and SimuCell3D (all C++-based) to simulate tissue development in 2D and 3D at cellular resolution.
SimuCell3D: 3D Simulation of Tissue Mechanics with Cell Polarization
Steve Runser, Roman Vetter, and Dagmar Iber
external pagebioRxivcall_made (2023), external pageTweetorialcall_made
PolyHoop: Soft particle and tissue dynamics with topological transitions.
Roman Vetter, Steve Runser, and Dagmar Iber
external pageComputer Physics Communicationscall_made (2024), external pageTweetorialcall_made
LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems.
Tanaka S, Sichau D, Iber D, external pageBioinformaticscall_made, 2015.
external pageDocumentationcall_made; external pageDownloadcall_made
external pageMOCCASINcall_made
We developed MOCCASIN to translate MATLAB ODE models into SBML.
Simulating Organogenesis in COMSOL: Tissue Mechanics
Peters, M and Iber, D,
external pageProceedings of COMSOL Conferencecall_made 2017 Rotterdam
Simulating organogenesis in COMSOL: comparison of methods for simulating branching morphogenesis
LD Wittwer, M Peters, S Aland, D Iber
external pageProceedings of COMSOL Conferencecall_made 2017 Rotterdam
Simulating organogenesis in COMSOL: Phase-field based simulations of embryonic lung branching morphogenesis
LD Wittwer, R Croce, S Aland, D Iber
external pageProceedings of COMSOL Conferencecall_made 2016 Munich
Simulating Organogenesis in COMSOL: Image-based Modeling
Z Karimaddini, E Unal, D Menshykau, D Iber
external pageProceedings of COMSOL Conferencecall_made, 2014
Simulating organogenesis in COMSOL: cell-based signaling models
J Vollmer, D Menshykau, D Iber
external pageProceedings of COMSOL Conferencecall_made, 2013
Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models
D Menshykau, S Adivarahan, P Germann, L Lermuzeaux, D Iber
external pageProceedings of COMSOL Conferencecall_made, 2013
Simulating organogenesis with COMSOL: Deforming and interacting domains
D Menshykau, D Iber
external pageProceedings of COMSOL Conferencecall_made 2012
Simulating organogenesis in COMSOL
P Germann, D Menshykau, S Tanaka, D Iber
external pageProceedings of COMSOL Conferencecall_made, 2011