CellModeller Structure - cellmodeller/CellModeller GitHub Wiki

CellModeller is a GPU-accelerated multicellular modelling framework that can be used to simulate multicellular systems, such as bacterial colonies and plants. This latest release (v4) comes with modules designed to model bacterial colonies.

CellModeller is organised into 4 main parts (or modules):

https://github.com/HaseloffLab/CellModeller/blob/master/Doc/modules.png

These modules are contained within a Simulator object, which runs your simulation.

A CellModeller 'model' is just python code that contains set of parameters and rules that define your simulation. A model consists of functions that initialise a Simulator object with the required modules, appropriate parameters, initial conditions, and the rules the govern your system.

Bacterial cells properties are contained in the CellStates object - this is a dictionary linking the id of each cell to its properties, which is the physical information (position, size), growth rates, and other optional items depending on your simulation (eg. cell type, color, intracellular chemical concentrations...).

For a step-by-step guide on what exactly each part in the model file does and how to write your own for your specific simulation needs, please see our Tutorials.