Secretion Plugin (legacy version)

In earlier version os of CC3D secretion was part of PDE solvers. We still support this mode of model description however, starting in 3.5.0 we developed separate plugin which handles secretion only. Via secretion plugin we can simulate cellular secretion of various chemicals. The secretion plugin allows users to specify various secretion modes in the CC3DML file – CC3DML syntax is practically identical to the SecretionData syntax of PDE solvers. In addition to this Secretion plugin allows users to maniupulate secretion properties of individual cells from Python level. To account for possibility of PDE solver being called multiple times during each MCS, the Secretion plugin can be called multiple times in each MCS as well. We leave it up to user the rescaling of secretion constants when using multiple secretion calls in each MCS. Note:Secretion for individual cells invoked via Python will be called only once per MCS.

By default ExtraTimesPerMC is set to 0 - meaning no extra calls to Secretion plugin per MCS.

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)


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.secreteInsideCellAtCOM(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:

8. 
   secreteInsideCell – this is equivalent to secretion in every pixel belonging to a cell
   
9. 
   secreteInsideCellAtBoundary – secretion takes place in the pixels belonging to the cell boundary
   
10. 
    secreteInsideCellAtBoundary – secretion takes place in pixels which are outide the cell but in contact with cell boundary pixels
    
11. 
    secreteInsideCellAtCOM – secretion at the center of mass of the cell
    

As you may infer from above modes 1, 2 and 3 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