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

SimuCell3D: 3D Simulation of Tissue Mechanics with Cell Polarization
Steve Runser, Roman Vetter, and Dagmar Iber
external pagebioRxiv (2023), external pageTweetorial

PolyHoop

PolyHoop: Soft particle and tissue dynamics with topological transitions. 
Roman Vetter, Steve Runser, and Dagmar Iber
external pageComputer Physics Communications (2024), external pageTweetorial

LBIBCell

LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems.
Tanaka S, Sichau D, Iber D, external pageBioinformatics, 2015.

external pageDocumentationexternal pageDownload

 

MOCCASIN

external pageMOCCASIN

We developed MOCCASIN to translate MATLAB ODE models into SBML.  

COMSOL

COMSOL
We are developing COMSOL applications for image-based modelling.
 

Simulating Organogenesis in COMSOL: Tissue Mechanics
Peters, M and Iber, D,
external pageProceedings of COMSOL Conference 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 Conference 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 Conference 2016 Munich

Simulating Organogenesis in COMSOL: Image-based Modeling
Z Karimaddini, E Unal, D Menshykau, D Iber
external pageProceedings of COMSOL Conference, 2014

Simulating organogenesis in COMSOL: cell-based signaling models
J Vollmer, D Menshykau, D Iber
external pageProceedings of COMSOL Conference, 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 Conference, 2013

Simulating organogenesis with COMSOL: Deforming and interacting domains
D Menshykau, D Iber
external pageProceedings of COMSOL Conference 2012

Simulating organogenesis in COMSOL
P Germann, D Menshykau, S Tanaka, D Iber
external pageProceedings of COMSOL Conference, 2011

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