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 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.

Introduction Larvae of the nematode Caenorhabditis elegans aggregate into clusters of several hundred moving individuals when starved during their first larval stage (see video below). Avery et al. proposed that starved larvae produce and respond chemotactically to two diffusible chemical signals, a short-range attractant and a longer range repellent.

Introduction Comparison of spatio-temporal model output to experimental measurements or between model variants all require the application of summary statistics. For multicellular models, statistical properties of the cell configuration at given times or across time are of interest and Morpheus provides some Analysis/Trackers for that: CellTracker, DisplacementTracker, ClusteringTracker and ContactLogger.

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.

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.

This multiscale mechanistic liver lobule model is composed of various interacting cell types, such as hepatocytes, residential Kupffer cells and macrophages. It captures hepatocellular acetaminophen (APAP) metabolism, DNA damage response activation, necrotic cell death, macrophage recruitment and the regulation of hepatocellular senescence and proliferation, with qualitatively different outcomes as a function of the initial APAP concentration in blood plasma.

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.