Multicellular modelling framework, created by Tim Rudge, PJ Steiner, and Jim Haseloff, University of Cambridge
This fork of CellModeller can simulate growth in microfluidic traps. This is permitted by the following functionalities:
- Cell removal from the simulation
- PDE solver with user-defined boundary conditions
Cell removal is handled by deleting the cell id from sim.CellStates and excluding these cells from the biophysics handling. See this tutorial.
Scalar fields are handled by FEniCS 2019.1.0, an open-source PDE solver. The CellModeller engine and FEniCS solver are fully coupled. Please download FEniCS from their website. Try running this tutorial.
Cells and fields can be visualized simultaneously in Paraview by converting .pickle files to .vtp format. Some parts of this are still in progress.
All the above updates are based on the work of @WilliamPJSmith.
/!\ Simulations interfaced with FEniCS cannot be run in the GUI.
This fork is interfaced to work with pyabc. See this tutorial for a minimal example.
To setup a calibration, setup the setparams function like so in the CellModeller module file:
def setparams(param_dict):
global your_parameter
your_parameter = param_dict['your_parameter']
This defines which parameters will be calibrated. Afterwards, setup the the ABC simulation script in a similar fashion to the tutorials in the pyabc documentation
A term for reaction has been added to the Signalling module.