Model for the interaction of Wnt and Hh as published in Kolbe et al.: Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human, Cell Reports, 29,4553,
For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix:
Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985
The model format is MorpheusML that can readily be loaded and run in the free and open source software
Morpheus is the modelling and simulation framework for multicellular systems biology developed at Technische Universität Dresden.
Manual, examples and binaries for Windows, Linux, MacOS at: https://morpheus.gitlab.io
Open source code at: https://gitlab.com/morpheus.lab/morpheus
Code for the bile flow model in Segovia-Miranda et al.: Three-dimensional spatially resolved geometrical and functional models of human liver tissue reveal new aspects of NAFLD progression (https://www.nature.com/articles/s41591-019-0660-7)
See the README file in the link for details installing and running the code.
The model is adapted from A.P. Kupinski, I. Raabe, M. Michel, D. Ail, L. Brusch, T. Weidemann, C. Bökel (2013) Phosphorylation of the Smo tail is controlled by membrane localization and is dispensable for clustering, J. Cell Sci., 126, 20, 4684-4697 doi: 10.1242/jcs.128926
The model format is MorpheusML that can readily be loaded and run in Morpheus: https://imc.zih.tu-dresden.de//wiki/morpheus
This model describes a core process during endocytosis. Intracellular vesicles called early endosomes contain the endocytosed cargo, e.g. signaling components like growth factors and RTKs, pathogens like viruses and nutrients like iron in transferrin. Early endosomes form an interacting pool of thousands of vesicles and jointly constitute the sorting and transport machinery in the endocytic pathway. Together with the cargo, membrane components travel to other compartments of the pathway which