Multicellular Model

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.

Diversity in simulation methods poses challenges in reproducibility, modularity, reusability, and integration within multi-scale simulation. This workshop …

How does morphogen transport in a growing tissue feed back on tissue growth through morphogen signaling and cell division? Introduction The Drosophila wing primordium is a two-dimensional epithelial tissue that grows in response to the concentration profile of the morphogen Dpp (see Fig.

How is the right islet size established during zebrafish pancreas development? Introduction Beta cells in the developing pancreas of zebrafish divide rapidly between 5 and 30 days post fertilization (dpf) and additional beta cells are recruited to the islet.

How can a densely packed PSM tissue mechanically split up into a string of separate somites? Introduction Somitogenesis is the defining developmental process of vertebrate species and essential for the segmentation of the main body axis and, among other repetitive structures, the formation of vertebrae.

Hepatocyte–sinusoid alignment (HSA) causes asymmetric shapes in early hepatocellular tumors. Introduction The mammalian liver is subdivided into lobes and further into thousands of hexagonal columns, called lobules, which act in parallel.

Hepatocyte–sinusoid alignment (HSA) supports the coordination of hepatocytes during liver regeneration after damage by carbon tetrachloride. Introduction The regenerative capacity of the mammalian liver did already inspire the fate of Prometheus in Greek Myth but it still poses many questions today that call for spatio-temporal multicellular modeling.

Introduction The mass-conserving secretion and uptake of (signaling) molecules by cells can in Morpheus be achieved with Mappers and scaling fluxes by cell.volume. The intracellular amount of signal may trigger a change in a state variable that could downstream change cell behaviors.

This model also requires the separate file Population_M.csv with the list of lattice nodes where cells shall be initialized. Introduction Initializing the spatial configuration of cells is a key step of every simulation and Morpheus offers all the flexibility for this: