VolumeConstraint

Examples Menu To explore the potential and modeling features, it is the best to learn by example. Morpheus comes with a range of fully functional example models showcasing a number of model formalism and modeling features.

To show SBML support in Morpheus as of version 2.1 in practice, we give a step-by-step example of how to download, import and extend an SBML model. 1. Get an SBML Model from BioModels First, we browse the BioModels model repository and select a model.

Converting the model from the previous chapter into a 2D model is trivial in Morpheus. In the Space section, you only need to change the Size of the Lattice to e.

Let’s go through an example. We’ll construct a model in which an intracellular cell cycle network (ODE) regulates the division of motile cells which (CPM) release a diffusive cytokine (PDE) which, in turn, controls the cell cycle (ODE).

Introduction This model shows the original cellular Potts model (a.k.a. Glazier-Graner model) of cell sorting based on the Steinberg’s differential adhesion hypothesis. Yellow cells engulf the red cells as a result of differential adhesion.

Simulations of four types of cells with different shapes to demonstrate how the combined target volume, surface area, and medium contact interaction determine the shape of the cell Introduction By setting the volume, surface, and length constraints, a CPM simulation can produce a variety of cell shapes.

A simplified version of the Morpheus cell sorting example Introduction A simplified version of the Morpheus built-in example of M0021"cell sorting showing the effect of cell-cell and cell-medium contact energies on the tissue configuration.

Time sequence showing the changing shape of a CPM cell Introduction Not all cell shapes are circular. In this example, a single cell undergoes a whole series of deformations resulting in the development of irregular cell shapes.

Example demonstrating how adhesion energies affect cell shape and the cell-cell contact region Introduction We simulate two CPM cells of the same type to demonstrate how adhesion energies affect cell shape and the cell-cell contact region.

The migration of zebrafish polster cells is oriented by the migration of follower cells, allowing robust long-range coordination of different cell populations. Introduction Collective cell migration is an important process during biological development and tissue repair.