Examples: Mitosis

Related: Mitosis

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The folder containing this simulation is

Demos/CompuCellPythonTutorial/steppableBasedMitosis.

File:

Demos/CompuCellPythonTutorial/steppableBasedMitosis/Simulation/steppableBasedMitosisSteppables.py

from PySteppables import *
from PySteppablesExamples import MitosisSteppableBase
import CompuCell

class VolumeParamSteppable(SteppableBasePy):
    def __init__(self, _simulator, _frequency=1):
        SteppableBasePy.__init__(self, _simulator, _frequency)

    def start(self):
        for cell in self.cellList:
            cell.targetVolume = 25
            cell.lambdaVolume = 2.0

    def step(self, mcs):
        for cell in self.cellList:
            cell.targetVolume += 1

class MitosisSteppable(MitosisSteppableBase):
    def __init__(self, _simulator, _frequency=1):
        MitosisSteppableBase.__init__(self, _simulator, _frequency)

        # 0 - parent child position will be randomized between mitosis event
        # negative integer - parent appears on the 'left' of the child
        # positive integer - parent appears on the 'right' of the child
        self.setParentChildPositionFlag(-1)

    def step(self, mcs):
        cells_to_divide = []
        for cell in self.cellList:
            if cell.volume > 50:
                cells_to_divide.append(cell)

        for cell in cells_to_divide:
            # to change mitosis mode leave one of the below lines uncommented
            self.divideCellRandomOrientation(cell)

    def updateAttributes(self):
        self.parentCell.targetVolume /= 2.0  # reducing parent target volume
        self.cloneParent2Child()

        if self.parentCell.type == self.CONDENSING:
            self.childCell.type = self.NONCONDENSING
        else:
            self.childCell.type = self.CONDENSING

Two steppables: VolumeParamSteppable and MitosisSteppable are the the essence of the above simulation. The first steppable initializes the volume constraint for all the cells present at T=0 MCS (only one cell) and then every 10 MCS (see the frequency with which VolumeParamSteppable in initialized to run - Demos/CompuCellPythonTutorial/steppableBasedMitosis/Simulation/steppableBasedMitosis.py) it increases the target volume of cells, effectively causing cells to grow.

from steppableBasedMitosisSteppables import VolumeParamSteppable
volumeParamSteppable=VolumeParamSteppable(sim ,10)
steppableRegistry.registerSteppable(volumeParamSteppable)

from steppableBasedMitosisSteppables import MitosisSteppable
mitosisSteppable=MitosisSteppable(sim, 10)
steppableRegistry.registerSteppable(mitosisSteppable)

The second steppable checks every 10 MCS (we can, of course, run it every MCS) if a cell has reached its doubling volume of 50. If it did, that cell is added to the list cells_to_divide. After construction of cells_to_divide is complete, we iterate over this list and divide all the cells within it.

Warning

It is important to divide cells outside the loop where we iterate over the entire cell inventory. If we keep dividing cells in this loop we are adding elements to the list over which we iterate and this might have unwanted side effects. The solution is to use a list of cells to divide as we did in the example.

Notice that we call self.divideCellRandomOrientation(cell) function to divide cells. Other modes of division are available as well and they are as follows:

self.divideCellOrientationVectorBased(cell,1,0,0)
self.divideCellAlongMajorAxis(cell)
self.divideCellAlongMinorAxis(cell)