CellModeller is a Python-based framework for modelling large-scale multi-cellular systems, such as biofilms, plant and animal tissue. We have developed models of cellular biophysics, gene regulation and other intracellular processes, and intercellular signalling. The idea of CellModeller is to create a system to simulate these models together in populations of growing and dividing cells.

CellModeller is open source and on Github. We're keen to get people involved, so please fork, pull-request, etc. You can also talk to us on the googlegroup.


Quick start

Clone the repository:

$ git clone https://github.com/HaseloffLab/CellModeller.git

Install the package (it is recommended to create a Conda or virtualenv environment first):

$ cd CellModeller; pip install -e .

Now you should create a folder to store the results of simulations:

$ mkdir -p ~/cellmodeller/data

You can now load and run models, either using the GUI or batch mode:

$ python CellModeller/Scripts/CellModellerGUI.py 

Take a look at the user guide and examples (also in CellModeller/Examples).


$ python CellModeller/Scripts/batch.py 

Take a look at the batch script (cellmodeller/Scripts/batch.py) to see a simple example.