Problems in biology are intrinsically multi-scale, with processes occurring on many disparate spatial and temporal scales. Here we present a multiscale framework for the mathematical modelling of biological systems. Utilising the natural structural unit of the cell, the framework consists of three main scales: the tissue level (macro-scale); the cell level (meso-scale); and the sub-cellular...
Multicellular biological systems span many spatial and temporal scales, yet models of these systems are often developed in isolation, using different assumptions, algorithms, and software frameworks. Vivarium is an open-source compositional framework designed to make these models interoperable by allowing independently developed components to be connected through standardized interfaces and...
The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised frameworks users need to master before they can run simulations. Artistoo (Artificial Tissue Toolbox) is a JavaScript library for building...
CompuCell3D is an open-source multiscale modeling environment for multicellular systems that combines biological realism, computational flexibility, and ease of learning. Based on the cellular Potts/Glazier-Graner-Hogeweg formalism, it supports explicit dynamic cell shape, adhesion, motility, growth, elastic solid-like junctions, filopodia, extracellular transport, and coupling to...
Collaborative modeling and simulation become increasingly important to study complex developmental processes across molecular to organism scales. To support interdisciplinary workflows in quantitative multicellular biology we designed the extensible open-source modeling framework Morpheus. It is centered around the cellular Potts model (cell behavior), allows for tight integration with...
PhysiCell (physicell.org) is an open source physics-based multicellular modeling framework. A cell is defined by a (off-lattice) centroid and volume and several phenotypic parameters that define its behavior (cell cycle, death, mechanics, motility, secretion, etc). It is bundled together with the BioFVM diffusion solver for cell secretion/uptake. PhysiCell has many predefined (but modifiable)...
Cellular tissue simulations can be computationally demanding, which restricts them to simplified cell geometries and low spatial resolution. Here I present two recently introduced cell-based simulation programs written in C++, PolyHoop and SimuCell3D, which are designed to efficiently model cellular tissues with detailed subcellular resolution. PolyHoop simulates cellular monolayers in 2D...
Multicellular simulations have become indispensable in understanding complex biological phenomena, from tissue development to disease progression. However, the diversity in simulation methods, ranging from agent-based models to lattice-free models and stochastic particle simulations, poses challenges in terms of reproducibility, modularity, reusability, and integration within multi-scale...
