CELL-BASED TISSUE SIMULATION SOFTWARE
To simulate the control of tissue development at cellular resolution, we are developing LBIBCell. Here we can couple the biophysical details of the tissue dynamics with the PDE models for the regulatory networks.
PUBLICATIONS
PUBLICATIONS
- Tanaka S, Sichau D, Iber D, submitted.
COMSOL-BASED FEM APPROACHES
We are using COMSOL to simulate 2D and 3D models of organogenesis on growing embryonic domains. To this end, we developed approaches to obtain the embryonic shapes and displacement fields from imaging data and to use them in COMSOL. Moreover, we optimised COMSOL to solve our complex biological network models efficiently on these realistic domains with subdomains, and to automise the process of parameter estimation.
JOURNAL PUBLICATIONS
CONFERENCE PROCEEDINGS
Book Chapters
JOURNAL PUBLICATIONS
- Schwaninger CA, Menshykau D, Iber D, Simulating Organogenesis: Algorithms for the Image-based Determination of Growth Fields. ACM Transactions on Modeling and Computer Simulation (TOMACS) (2014) accepted
CONFERENCE PROCEEDINGS
- Karimaddini Z, Ünal E, Menshykau D and Iber D, Simulating Organogenesis in COMSOL: Image-based Modeling, Proceedings of COMSOL Conference 2014, Cambridge
- Velten B, Uenal E and Iber D (2014) Image-based Parameter Inference for Spatio-temporal models of Organogenesis.
NOLTA 2014 (Luzern, CH) International Symposium on Nonlinear Theory & its Applications - Menshykau D, Adivarahan S, Germann P, Lemereux L and Iber D (2013) Simulating Organogenesis in COMSOL: Parameter Optimization for PDE-based models. Proceedings of COMSOL Conference 2013, Rotterdam
- Vollmer J, Menshykau D, and Iber D (2013) Simulating Organogenesis in COMSOL: Cell-based Signaling Models. Proceedings of COMSOL Conference 2013, Rotterdam
- Adivarahan S, Menshykau D, Michos O and Iber D (2013) Dynamic Image-Based Modelling of Kidney Branching Morphogenesis. Lecture Notes in Computer Science (Springer), Computational Methods in Systems Biology (CMSB) 2013 IST Austria
- Menshykau D and Iber D (2012) Simulating Organogenesis in Comsol: Deforming and Interacting Domains, Proceedings of COMSOL Conference 2012
- Germann P, Tanaka S, Menshykau D, and Iber D (2011) Simulating Organogenesis in Comsol, Proceedings of COMSOL Conference 2011
Book Chapters
- Iber D, Tanaka S, Fried P, Germann G and Menshykau D Simulating Tissue Morphogenesis and Signaling, Springer Book Series: Methods in Molecular Biology. Book Title: Tissue Morphogenesis: Methods and Protocols. Editor: Celeste Nelson, in press