Models

What is a Model?
14 Models visible to you, out of a total of 18

The model studies the influence of hepatocyte–sinusoid alignment (HSA), i.e. the orientation of the division plane such that daughter hepatocytes align with nearby sinusoids, on the shape of tumor nodules in liver lobules. It employs the structure of the model ‘Liver Regeneration from CCl4’ (https://seek.lisym.org/models/19).

Originally, Höhme et al. (https://doi.org/10.1007/s11538-017-0375-1) employed a center-based model. Here, the model is encoded in the standardized language MorpheusML. ...

Creators: Diego Jahn, Michael Kücken, Lutz Brusch

Submitter: Diego Jahn

In the experimental paradigm of CCl4 intoxication of mice, hepatocytes around the central vein (located in the center of an idealized hexagonal liver lobule) are dying and are subsequently replaced by new hepatocytes, largely through activation of proliferation in the remaining hepatocytes.

Alignment of daughter hepatocytes along the orientation of the closest sinusoid, a process which is named hepatocyte-sinusoid alignment (HSA), was proposed by Höhme et al. (https://doi.org/10.1073/pnas.0909374107) ...

Creators: Diego Jahn, Michael Kücken, Lutz Brusch

Submitter: Diego Jahn

ODE model describes dynamics of IFNalpha-induced signaling in Huh7.5 cells for a time scale up to 32 hours after stimulation with IFNalpha. The model consists of an IFN receptor model, formation/degradation and cytoplasmic/nuclear shuttling of STAT1-homodimers, STAT1-STAT2-heterodimers and STAT1-STAT2-IRF9 (ISGF3) complexes. On top, formation of feedback proteins STAT1, STAT2, IRF9, USP18, SOCS1, SOCS3 and IRF2 and corresponding influences on IFNalpha signaling dynamics was incorporated. The model ...

Creators: Jens Timmer, Ursula Klingmüller, Daniel Seehofer, Marcus Rosenblatt, Krishna Kumar Tiwari, Frédérique Kok

Submitter: Olga Krebs

No description specified

Creator: Andreas Weidemann

Submitter: Andreas Weidemann

This model was used in the Modeling Workshop at the 2nd LiSyM-Cancer Status Seminar.

Creator: Lutz Brusch

Submitter: Lutz Brusch

Taken from https://github.com/Benchmarking-Initiative/Benchmark-Models See the github repository for license Import and execute the model in d2d

Creator: Jens Timmer

Submitter: Daniel Lill

Taken from https://github.com/Benchmarking-Initiative/Benchmark-Models License according to the github repository's license Import and execute with d2d

Creators: Jens Timmer, Lorenza D'Alessandro, S.Sobotta, A. Raue, J. Vanlier

Submitter: Daniel Lill

not yet calibrated, not yet reduced

Creators: Daniel Lill, Viktor Makarenko

Submitter: Daniel Lill

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 https://doi.org/10.1242/jcs.128926

The model format is MorpheusML that can readily be loaded and run in Morpheus: https://morpheus.gitlab.io

Creator: Lutz Brusch

Submitter: Lutz Brusch

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,

https://doi.org/10.1016/j.celrep.2019.11.104

Creators: Michael Kücken, Lutz Brusch

Submitters: Lutz Brusch, Michael Kücken

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 ...

Creator: Lutz Brusch

Submitter: Lutz Brusch

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

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.

Creators: Michael Kücken, Lutz Brusch

Submitter: Michael Kücken

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 ...

Creator: Lutz Brusch

Submitter: Lutz Brusch

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