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
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Creator: Lutz Brusch
Submitter: Lutz Brusch
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
Organism: Mus musculus
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
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
Creators: Lutz Brusch, Jörn Starruß, Walter de Back, Andreas Deutsch
Submitter: Lutz Brusch
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Abstract (Expand)
Authors: S. Brunak, C. Bjerre Collin, K. Eva O Cathaoir, M. Golebiewski, M. Kirschner, I. Kockum, H. Moser, D. Waltemath
Date Published: 24th Jul 2020
Publication Type: Journal
PubMed ID: 32827396
Citation: J Integr Bioinform. 2020 Jul 24;17(2-3). pii: /j/jib.2020.17.issue-2-3/jib-2020-0006/jib-2020-0006.xml. doi: 10.1515/jib-2020-0006.
Abstract (Expand)
Authors: Kirstin Meyer, Hernan Morales‐Navarrete, Sarah Seifert, Michaela Wilsch‐Braeuninger, Uta Dahmen, Elly M Tanaka, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial
Date Published: 24th Feb 2020
Publication Type: Not specified
Citation: Mol Syst Biol 16(2) : 186
Abstract (Expand)
Authors: Oleksandr Ostrenko, Jochen Hampe, Lutz Brusch
Date Published: 1st Dec 2019
Publication Type: Not specified
DOI: 10.1038/s41598-019-40853-7
Citation: Sci Rep 9(1) : 823
Abstract (Expand)
Authors: Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini
Date Published: 4th Dec 2017
Publication Type: Not specified
DOI: 10.1371/journal.pcbi.1005865
Citation: PLoS Comput Biol 13(12) : e1005865
Abstract (Expand)
Authors: Kirstin Meyer, Oleksandr Ostrenko, Georgios Bourantas, Hernan Morales-Navarrete, Natalie Porat-Shliom, Fabian Segovia-Miranda, Hidenori Nonaka, Ali Ghaemi, Jean-Marc Verbavatz, Lutz Brusch, Ivo Sbalzarini, Yannis Kalaidzidis, Roberto Weigert, Marino Zerial
Date Published: 1st Mar 2017
Publication Type: Not specified
DOI: 10.1016/j.cels.2017.02.008
Citation: Cell Systems 4(3) : 277
Computational modeling and simulation become increasingly important for Systems Medicine. A number of corresponding software tools have been developed but require scientists to encode their models in an imperative programming language. Morpheus [1,2], on the other hand, is an extensible open-source software framework that is entirely based on declarative modeling. It uses the domain-specific language MorpheusML to define multicellular models through a user-friendly GUI and has since proven
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Creators: Lutz Brusch, Michael Kücken
Submitter: Lutz Brusch
Poster at SBMC 2018
Creators: Lars Ole Schwen, Lars Kuepfer, Ahmed Ghallab, Jan Hengstler, Tobias Preusser, Raymond Reif
Submitter: Lars Ole Schwen