Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Cancer biology involves complex, dynamic interactions between cancer cells and their
tissue microenvironments. Single-cell effects are critical drivers of clinical progression …

Abstract Background and Objective: Cardiac electrophysiology is a medical specialty with a
long and rich tradition of computational modeling. Nevertheless, no community standard for …

Many multicellular systems problems can only be understood by studying how cells move,
grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many …

The dynamic behavior of epithelial cell sheets plays a central role during numerous
developmental processes. Genetic and imaging studies of epithelial morphogenesis in a …

We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of
confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail …

Highly resolved spatial data of complex systems encode rich and nonlinear information.
Quantification of heterogeneous and noisy data—often with outliers, artifacts, and …

In this paper we present an overview of agent-based models that are used to simulate
mechanical and physiological phenomena in cells and tissues, and we discuss underlying …

The coordinated behaviour of populations of cells plays a central role in tissue growth and
renewal. Cells react to their microenvironment by modulating processes such as movement …

Morpheus is a modeling environment for the simulation and integration of cell-based models
with ordinary differential equations and reaction-diffusion systems. It allows rapid …