Figure 1.

AT II analogue components and system architecture. Experiment manager is a system-level agent that prepares parameter files, manages experiment execution and processes output data for analysis and summary. Observer is an agent that tracks individual cell activities and measures culture attributes. Culture represents an arbitrary section of an in vitro cell culture. It maintains a two-dimensional hexagonal grid within which cells, matrix and free space objects interact. Those three object types correspond to, respectively, AT II cells, extracellular matrix and the region (e.g. cyst lumen) devoid of cells and extracellular matrix. Matrix and free space are passive objects. Cells are quasi-autonomous agents with a set of axioms and decision logic that determine their action based on their internal state and neighbouring object configurations. Cluster represents a coherent aggregate of two or more cells and can include free space. Cells and clusters can call on different migration modes: random and factor-responsive. Diffuser is an extension to the culture space to simulate factor diffusion. It uses a second hexagonal grid. Culture graphical user interface (GUI) provides features to visualize and probe culture during simulation. The system was implemented using MASON, which provides standard libraries, object classes and methods for multi-agent, discrete event simulation (Luke et al. 2005).