Prof. Uri Nevo
Cell Studio –
Agent Based Modelling (ABM) platform
Cell studio is an agent-based modelling system, originally designed for immunological scenarios, based on gaming and 3-D visualization tools. The system enables researchers with little mathematical or programming background to create dynamic 3D cellular scenario using a simple and friendly graphical user interface.
The simulation is governed by a user-defined system of rules, with a simple mechanism where a set of events leads to a set of actions. The model is implemented as a hybrid agent-based simulation, in which each cell is an autonomous agent, with a set of properties and abilities (resulting in an inherent ‘state’), subject to biophysical laws, predefined rules of simulation and general environment constraints.
The main advantages of the system are its ability to apply any cell geometry and to dynamically visualize the diffusion and interactions of the molecules within the cells in real time. Using parallel and high-performance computing, the platform can simulate hundreds of thousands of agents/cells for extended biological time intervals, of the order of weeks.
(a) Outlines a set of rules for two types of agents, encompassing properties such as cell state, interactions with other cells, activation, receptor expressions, molecule secretion, as well as cell apoptosis or proliferation. These parameters can be pre-set and adjusted to align with specific biological properties.
(b) Explores complex populations of diverse cells and varying cell types. The ABM enables the simulation of different cells, providing a visual representation of their interactions.
(c) Illustrates a connection between two cells of different types, showcasing a specific interaction governed by predefined rules within the simulation.
(d) Illustrates the interaction among three cells, involving two distinct cell types. This process follows a predetermined set of rules that are established before initiating the simulation, and these rules play a crucial role in governing interactions during the simulation.