111Equation Chapter 1 Section 1 CompuCell3d reference Manual Version 4

Mitosis Plugin

Mitosis plugin carries out cell division into two cells once the parent cell reaches critical volume (DoublingVolume). The two cells after mitosis will have approximately the same volume although it cannot be guaranteed in general case if the parent cell is fragmented. One major problem with Mitosis plugin is that after mitosis the attributes of the offspring cell might not be initialized properly. By default cell type of the offspring cell will be the same as cell type of parent and they will also share target volume. All other parameters for the new cell remain uninitialized.

Every time a cell reaches DoublingVolume it will undergo the mitosis and the offspring cell will inherit type and target volume of the parent. If this simple behavior is unsatisfactory consider use Python scripting to implement proper mitotic divisions of cells.

24. Secretion / SecretionLocalFlex Plugin

or as:

The inclusion of the above code in the CC3DML will allow users to implement secretion for individual cells from Python. Note:Secretion for individual cells invoked via Python will be called only once per MCS.

Important: Secretion plugin can be used to implement secretion by cell type however we strongly advise against doing so. Defining secretion by cell-type in the Secretion plugin will lead to performance degradation on multi-core machines. Please see section below for more information if you are still interested in using secretion by cell-type inside Secretion plugin

Typical use of secretion from Python is dempnstrated best in the example below:

def __init__(self,_simulator,_frequency=1):

def step(self,mcs):

attrSecretor=self.getFieldSecretor("ATTR")

for cell in self.cellList:

if cell.type==3:

attrSecretor.secreteInsideCell(cell,300)

attrSecretor.secreteInsideCellAtBoundary(cell,300)

attrSecretor.secreteOutsideCellAtBoundary(cell,500)

attrSecretor.secreteInsideCellAtCOM(cell,300)

elif cell.type==2:

attrSecretor.secreteInsideCellConstantConcentration(cell,300)

Remark: Instead of using SteppableBasePy class we are using SecretionBasePy class. The reason for this is that in order for secretion plugin with secretion modes accessible from Python to behave exactly as previous versions of PDE solvers (where secretion was done first followed by “diffusion” step) we have to ensure that secretion steppable implemented in Python is called before each Monte Carlo Step, which implies that it will be also called before “diffusing” function of the PDE solvers. SecretionBasePy sets extra flag which ensures that steppable which inherits from SecretionBasePy is called before MCS (and before all “regular’ Python steppables).

There is no magic to SecretionBasePy - if you still want to use SteppableBasePy as a base class for secretion (or for that matter SteppablePy) do so, but remember that you need to set flag:

def __init__(self,_simulator,_frequency=1):

def step(self,mcs):

attrSecretor=self.getFieldSecretor("ATTR")

for cell in self.cellList:

if cell.type==3:

attrSecretor.secreteInsideCell(cell,300)

attrSecretor.secreteInsideCellAtBoundary(cell,300)

attrSecretor.secreteOutsideCellAtBoundary(cell,500)

attrSecretor.secreteOutsideCellAtBoundaryOnContactwith(cell,500,[2,3])

attrSecretor.secreteInsideCellAtCOM(cell,300)

attrSecretor.uptakeInsideCellAtCOM(cell,300,0.2)

elif cell.type==2:

attrSecretor.secreteInsideCellConstantConcentration(cell,300)

The secretion of individual cells is handled through Field Secretor objects. Field Secretor concenpt is quite convenient because the amoun of Python coding is quite small. To secrete chemical (this is now done for individual cell) we first create field secretor object, attrSecretor=self.getFieldSecretor("ATTR"), which allows us to secrete into field called ATTR.

Then we pick a cell and using field secretor we simulate secretion of chemical ATTR by a cell:
attrSecretor.secreteInsideCell(cell,300)
Currently we support 6 secretion modes for individual cells:

1. 
   secreteInsideCell – this is equivalent to secretion in every pixel belonging to a cell
   
2. 
   secreteInsideCellConstantConcentration – this is equivalent to secretion in every pixel belonging to a cell and setting concentration to fixed, constant level
   
3. 
   secreteInsideCellAtBoundary – secretion takes place in the pixels belonging to the cell boundary
   
4. 
   secreteInsideCellAtBoundaryOnContactWith - secretion takes place in the pixels belonging to the cell boundary that touches any of the cells listed as the last argument of the function call
   
5. 
   secreteOutsideCellAtBoundary – secretion takes place in pixels which are outside the cell but in contact with cell boundary pixels
   
6. 
   secreteOutsideCellAtBoundaryOnContactWith - secretion takes place in pixels which are outside the cell but in contact with cell boundary pixels and in contact with cells listed the last argument of the function call
   
7. 
   secreteInsideCellAtCOM – secretion at the center of mass of the cell
   

and 6 uptake modes:

1. 
   uptakeInsideCell – this is equivalent to uptake in every pixel belonging to a cell
   
2. 
   uptakeInsideCellAtBoundary – uptake takes place in the pixels belonging to the cell boundary
   
3. 
   uptakeInsideCellAtBoundaryOnContactWith - uptake takes place in the pixels belonging to the cell boundary that touches any of the cells listed as the last argument of the function call
   
4. 
   uptakeOutsideCellAtBoundary – uptake takes place in pixels which are outside the cell but in contact with cell boundary pixels
   
5. 
   uptakeOutsideCellAtBoundaryOnContactWith - uptake takes place in pixels which are outside the cell but in contact with cell boundary pixels and in contact with cells listed the last argument of the function call
   
6. 
   uptakeInsideCellAtCOM – uptake at the center of mass of the cell
   

Secretion functions use the following syntax

secrete*(cell,amount,list_of_cell_types)

Note that list_of_cell_types is used only for function which implement such functionality i.e. (secreteInsideCellAtBoundaryOnContactWith and secreteOutsideCellAtBoundaryOnContactWith)

Uptake functions use the following syntax

uptake*(cell,max_amount,relative_uptake,list_of_cell_types)

Note that list_of_cell_types is used only for function which implement such functionality i.e. (uptakeInsideCellAtBoundaryOnContactWith and uptakeOutsideCellAtBoundaryOnContactWith)

Important: The uptake works as follows: when available concentratin is greater than max_amount, then max_amount is subtracted from current_concentration, otherwise we subtract relative_uptake*current_concentration.

As you may infer from above, the modes 1-5 require tracking of pixels belonging to cell and pixels belonging to cell boundary. If you are not using modes 1-3 you may disable pipxel tracking by including