Speaker
Description
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 level (micro-scale), with interactions occurring between all scales. The cell level is central to the framework and cells are modelled as discrete interacting entities using one of a number of possible modelling paradigms, including lattice based models (cellular automata and cellular Potts) and off-lattice models (cell centre and vertex based representations). The sub-cellular level concerns numerous metabolic and biochemical processes represented by interaction networks rendered stochastically or into ODEs. The outputs from such systems influence the behaviour of the cell level affecting properties such as adhesion and also influencing cell mitosis and apoptosis. Tissue level behaviour is represented by field equations for nutrient or messenger concentration, with cells functioning as sinks and sources. This modular approach enables more realistic behaviour to be considered at each scale.
The multi-scale framework is implemented in an open source software library known as Chaste (https://chaste.github.io/). This software library consists of object orientated C++, developed using an agile development approach. All software is tested, robust, reliable and extensible. The library enables general simulations to be undertaken and includes tools to atomically curate and store simulation results expediting model development. In this talk we introduce the framework and give some key examples of its use.
