Resources
We have developed the C++-based software LBIBCell to simulate tissue development at cellular resolution. In collaboration with the group of Prof Chopard (Uni Geneva) we are working on an external page extension of LBIBCell to 3D geometries.
Tanaka S, Sichau D, Iber D, LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems. external page Bioinformatics, 2015.
We developed MOCCASIN to translate MATLAB ODE models into SBML.
MATLAB code for the methods described in
Geier F, Fengos G, Felizzi F and Iber D
Analysing and constraining signaling networks: parameter estimation for the user
external page Springer Book Series: Methods in Molecular Biology
Book Title: Computational Modeling of Signaling Networks (Editor Xuedong Liu)
MATLAB code for the methods described in
Adivarahan S, Menshykau D, Michos O and Iber D
Dynamic Image-Based Modelling of Kidney Branching Morphogenesis.
external page Spinger Lecture Notes in Computer Science
Computational Methods in Systems Biology (CMSB) 2013 IST Austria
C++ code for the methods described in
Anna Stopka, Marco Kokic and Dagmar Iber
Cell-based simulations of biased epithelial lung growth
Physical Biology, Bristol: IOP Publishing, 2019.
external page https://doi.org/10.1088/1478-3975/ab5613
C++ code for the methods described in
Anna Stopka, Marcelo Boareto, and Dagmar Iber
Cell-Based Simulations of Notch-Dependent Cell Differentiation on Growing Domains
BioRxiv, November 29, 2019, 859363.
external page https://doi.org/10.1101/859363