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.
- Leverages CPU and GPU parallelism via OpenCL and PyOpenCL.
- Simple model definition with Python.
- Solves ODEs and PDEs coupled to cellular growth and division.
- Cell behaviour rules scripted in Python.
- Simulate large populations of more than 100,000 cells in 3D.
- Published biophysical model of rod-shaped bacteria (Rudge et al. 2012, 2013)
- Plant cell biophysical models to come (Rudge/Haseloff 2005, Dupuy et al. 2010)
- Create constraints to simulate e.g. growth chambers, channels, surfaces.
- Create high-definition videos and beautiful PDF figures.
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.