def __init__(self,_simulator,_frequency, _params_container ):
self.statsReporter = StatsReporter()
self.params_container = _params_container
MitosisSteppableBase.__init__(self,_simulator, _frequency)
self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ,
## of the border between mitosis regions in the GZ (measured from the posterior)
r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0')
r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1')
r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2')
r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3')
self.r_mitosis_list=[r_mitosis_R0,r_mitosis_R1,r_mitosis_R2,r_mitosis_R3]
self.window = 500 # length of window in MCS (see above)
self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide
self.Vmax = 90 # maximum volume to which cells can grow
self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization
self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided
# Set r_grow for each region: pixels per MCS added to cell's volume
r_grow_R0=0
r_grow_R1=0
r_grow_R2=0
r_grow_R3=0.05
self.r_grow_list=[r_grow_R0,r_grow_R1,r_grow_R2,r_grow_R3]
# t_grow_R0=self.calculate_t_grow(r_mitosis_R0)
# t_grow_R1=self.calculate_t_grow(r_mitosis_R1)
# t_grow_R2=self.calculate_t_grow(r_mitosis_R2)
# t_grow_R3=self.calculate_t_grow(r_mitosis_R3)
# self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3]
self.fraction_AP_oriented=0.5
self.statsReporter.displayStats(['rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2, 'rg_R3', r_grow_R3])
def __init__(self, _simulator, _frequency, _params_container):
self.statsReporter = StatsReporter()
self.params_container = _params_container
MitosisSteppableBase.__init__(self, _simulator, _frequency)
self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ,
## of the border between mitosis regions in the GZ (measured from the posterior)
r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0')
r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1')
r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2')
r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3')
self.r_mitosis_list = [
r_mitosis_R0, r_mitosis_R1, r_mitosis_R2, r_mitosis_R3
]
self.window = 500 # length of window in MCS (see above)
self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide
self.Vmax = 90 # maximum volume to which cells can grow
self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization
self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided
# Set r_grow for each region: pixels per MCS added to cell's volume
r_grow_R0 = 0
r_grow_R1 = 0
r_grow_R2 = 0
r_grow_R3 = 0.05
self.r_grow_list = [r_grow_R0, r_grow_R1, r_grow_R2, r_grow_R3]
# t_grow_R0=self.calculate_t_grow(r_mitosis_R0)
# t_grow_R1=self.calculate_t_grow(r_mitosis_R1)
# t_grow_R2=self.calculate_t_grow(r_mitosis_R2)
# t_grow_R3=self.calculate_t_grow(r_mitosis_R3)
# self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3]
self.fraction_AP_oriented = 0.5
self.statsReporter.displayStats([
'rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2,
'rg_R3', r_grow_R3
])
class RegionalMitosis(MitosisSteppableBase):
def __init__(self,_simulator,_frequency, _params_container ):
self.statsReporter = StatsReporter()
self.params_container = _params_container
MitosisSteppableBase.__init__(self,_simulator, _frequency)
self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ,
## of the border between mitosis regions in the GZ (measured from the posterior)
r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0')
r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1')
r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2')
r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3')
self.r_mitosis_list=[r_mitosis_R0,r_mitosis_R1,r_mitosis_R2,r_mitosis_R3]
self.window = 500 # length of window in MCS (see above)
self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide
self.Vmax = 90 # maximum volume to which cells can grow
self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization
self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided
# Set r_grow for each region: pixels per MCS added to cell's volume
r_grow_R0=0
r_grow_R1=0
r_grow_R2=0
r_grow_R3=0.05
self.r_grow_list=[r_grow_R0,r_grow_R1,r_grow_R2,r_grow_R3]
# t_grow_R0=self.calculate_t_grow(r_mitosis_R0)
# t_grow_R1=self.calculate_t_grow(r_mitosis_R1)
# t_grow_R2=self.calculate_t_grow(r_mitosis_R2)
# t_grow_R3=self.calculate_t_grow(r_mitosis_R3)
# self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3]
self.fraction_AP_oriented=0.5
self.statsReporter.displayStats(['rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2, 'rg_R3', r_grow_R3])
def start(self):
self.y_EN_pos=self.find_posterior_EN_stripe()
self.y_EN_ant=self.find_anterior_EN_stripe()
self.y_GZ_border=self.find_y_GZ_mitosis_border()
for cell in self.cellList:
region=self.assign_cell_region(cell)
# self.initiate_cell_volume(cell) ## Initiates cells with new volumes to distribute mitoses in time
cellDict = CompuCell.getPyAttrib(cell)
cellDict["growth_timer"]=self.attach_growth_timer(cell) ## attached a countdown timer for cell growth
def step(self,mcs):
print 'Executing Mitosis Steppable'
mitosis_list=self.make_mitosis_list()
self.perform_mitosis(mitosis_list)
self.y_EN_pos=self.find_posterior_EN_stripe()
self.y_EN_ant=self.find_anterior_EN_stripe()
self.y_GZ_border=self.find_y_GZ_mitosis_border()
for cell in self.cellList:
self.assign_cell_region(cell)
self.grow_cell(cell)
# mitosis_list=self.make_mitosis_list()
# self.perform_mitosis(mitosis_list)
def perform_mitosis(self,mitosis_list):
for cell in mitosis_list:
if self.mitosisVisualizationFlag:
self.visualizeMitosis(cell) # change cell type to "Mitosing"
### Choose whether cell will divide along AP or random orientation
AP_divide=random()
if AP_divide <= self.fraction_AP_oriented:
self.divideCellOrientationVectorBased(cell,0,1,0)
else:
self.divideCellRandomOrientation(cell)
if self.mitosisVisualizationFlag:
self.mitosisVisualizationCountdown() # Maintains cell type as "Mitosing" for a set window of time (self.mitosisVisualizationWindow)
# UpdateAttributes is inherited from MitosisSteppableBase
# and it is called automatically by the divideCell() function
# It sets the attributes of the parent and daughter cells:
def updateAttributes(self):
parentCell=self.mitosisSteppable.parentCell
childCell=self.mitosisSteppable.childCell
childCell.targetVolume = childCell.volume
childCell.lambdaVolume = parentCell.lambdaVolume
childCell.targetSurface = childCell.surface
childCell.lambdaSurface = parentCell.lambdaSurface
parentCell.targetVolume = parentCell.volume
parentCell.targetSurface = parentCell.surface
childCell.type = parentCell.type
parentDict=CompuCell.getPyAttrib(parentCell)
childDict=CompuCell.getPyAttrib(childCell)
### Make a copy of the parent cell's dictionary and attach to child cell
for key, item in parentDict.items():
childDict[key]=deepcopy(parentDict[key])
def assign_cell_region(self,cell):
cellDict=CompuCell.getPyAttrib(cell)
yCM=cell.yCM/float(cell.volume)
if yCM > self.y_EN_ant: # if cell is anterior to EN stripes
cellDict["region"]=0
# if (cell.type!=4 and cell.type!=2): # if cell is not En or mitosing
# cell.type=1 # AnteriorLobe
elif yCM > self.y_EN_pos: # if cell is in EN-striped region
cellDict["region"]=1
if (cell.type!=2 and cell.type!=4): # if cell is not En or mitosing
cell.type=5 # Segmented
elif yCM > self.y_GZ_border: # if cell is in anterior region of GZ
cellDict["region"]=2
if (cell.type!=2 and cell.type!=4): # if cell is not En or mitosing
cell.type=3 #GZ
else: # if cell is in posterior region of GZ
cellDict["region"]=3
if cell.type!=4: #if cell is not mitosing
cell.type=3 # GZ
def initiate_cell_volume(self,cell):
phase=random() # chooses a phase between 0 and 1 to initialize cell volume
volume_difference=self.Vmin_divide - cell.volume
new_volume=phase*volume_difference + cell.volume
cell.targetVolume = new_volume
def attach_growth_timer(self,cell):
phase=random() # picks a random phase between 0 and 1 to initialize cell growth timer
growth_timer=phase
return growth_timer
def grow_cell(self,cell):
cellDict=CompuCell.getPyAttrib(cell)
region=cellDict["region"]
r_grow=self.r_grow_list[region]
if cellDict["growth_timer"] >= 1:
if cell.targetVolume<=self.Vmax:
cell.targetVolume+=int(cellDict["growth_timer"])
cellDict["growth_timer"]=0
else:
cellDict["growth_timer"]+=r_grow
def make_mitosis_list(self):
mitosis_list=[]
for cell in self.cellList:
cellDict=CompuCell.getPyAttrib(cell)
region=cellDict["region"]
mitosis_probability=self.r_mitosis_list[region]/self.window
if mitosis_probability>=random():
if cell.volume >= self.Vmin_divide:
mitosis_list.append(cell)
return mitosis_list
def find_posterior_EN_stripe(self):
y_EN_pos=9999
for cell in self.cellList:
if cell.type==2: # EN cell
yCM=cell.yCM/float(cell.volume)
if yCM < y_EN_pos:
y_EN_pos=yCM
return y_EN_pos
def find_anterior_EN_stripe(self):
y_EN_ant=0
for cell in self.cellList:
if cell.type==2: # EN cell
yCM=cell.yCM/float(cell.volume)
if yCM > y_EN_ant:
y_EN_ant=yCM
return y_EN_ant
def find_y_GZ_mitosis_border(self):
y_GZ_pos=self.find_posterior_GZ()
y_GZ_border=y_GZ_pos + self.y_GZ_mitosis_border_percent*(self.y_EN_pos-y_GZ_pos)
return y_GZ_border
def find_posterior_GZ(self):
y_GZ_pos=9999
for cell in self.cellList:
yCM=cell.yCM/float(cell.volume)
if yCM < y_GZ_pos:
y_GZ_pos=yCM
return y_GZ_pos
# def calculate_t_grow(self,r_mitosis):
# if r_mitosis > 0:
# t_cycle=self.window/r_mitosis # approx time to double volume, in MCS
# t_grow=2*t_cycle/self.V_divide # MCS per pixel growth
# else:
# t_grow=999999999
# return t_grow
def visualizeMitosis(self,cell):
cellDict=CompuCell.getPyAttrib(cell)
cellDict['mitosisVisualizationTimer']=self.mitosisVisualizationWindow
cellDict['returnToCellType']=cell.type
cell.type = 4 # set to mitosing cell
def mitosisVisualizationCountdown(self):
for cell in self.cellList:
if cell.type==4: # if Mitosis cell
cellDict=CompuCell.getPyAttrib(cell)
if cellDict['mitosisVisualizationTimer']<=0:
cell.type=cellDict['returnToCellType']
else:
cellDict['mitosisVisualizationTimer']-=1
class RegionalMitosis(MitosisSteppableBase):
def __init__(self, _simulator, _frequency, _params_container):
self.statsReporter = StatsReporter()
self.params_container = _params_container
MitosisSteppableBase.__init__(self, _simulator, _frequency)
self.y_GZ_mitosis_border_percent = 0.5 ## The position, in fraction of the GZ (from posteriormost EN stripe to posterior of GZ,
## of the border between mitosis regions in the GZ (measured from the posterior)
r_mitosis_R0 = self.params_container.getNumberParam('r_mitosis_R0')
r_mitosis_R1 = self.params_container.getNumberParam('r_mitosis_R1')
r_mitosis_R2 = self.params_container.getNumberParam('r_mitosis_R2')
r_mitosis_R3 = self.params_container.getNumberParam('r_mitosis_R3')
self.r_mitosis_list = [
r_mitosis_R0, r_mitosis_R1, r_mitosis_R2, r_mitosis_R3
]
self.window = 500 # length of window in MCS (see above)
self.Vmin_divide = 60 # minimum volume, in pixels, at which cells can divide
self.Vmax = 90 # maximum volume to which cells can grow
self.mitosisVisualizationFlag = 1 # if nonzero, turns on mitosis visualization
self.mitosisVisualizationWindow = 100 # number of MCS that cells stay labeled as having divided
# Set r_grow for each region: pixels per MCS added to cell's volume
r_grow_R0 = 0
r_grow_R1 = 0
r_grow_R2 = 0
r_grow_R3 = 0.05
self.r_grow_list = [r_grow_R0, r_grow_R1, r_grow_R2, r_grow_R3]
# t_grow_R0=self.calculate_t_grow(r_mitosis_R0)
# t_grow_R1=self.calculate_t_grow(r_mitosis_R1)
# t_grow_R2=self.calculate_t_grow(r_mitosis_R2)
# t_grow_R3=self.calculate_t_grow(r_mitosis_R3)
# self.t_grow_list=[t_grow_R0,t_grow_R1,t_grow_R2,t_grow_R3]
self.fraction_AP_oriented = 0.5
self.statsReporter.displayStats([
'rg_RO', r_grow_R0, 'rg_R1', r_grow_R1, 'rg_R2', r_grow_R2,
'rg_R3', r_grow_R3
])
def start(self):
self.y_EN_pos = self.find_posterior_EN_stripe()
self.y_EN_ant = self.find_anterior_EN_stripe()
self.y_GZ_border = self.find_y_GZ_mitosis_border()
for cell in self.cellList:
region = self.assign_cell_region(cell)
# self.initiate_cell_volume(cell) ## Initiates cells with new volumes to distribute mitoses in time
cellDict = CompuCell.getPyAttrib(cell)
cellDict["growth_timer"] = self.attach_growth_timer(
cell) ## attached a countdown timer for cell growth
def step(self, mcs):
print 'Executing Mitosis Steppable'
mitosis_list = self.make_mitosis_list()
self.perform_mitosis(mitosis_list)
self.y_EN_pos = self.find_posterior_EN_stripe()
self.y_EN_ant = self.find_anterior_EN_stripe()
self.y_GZ_border = self.find_y_GZ_mitosis_border()
for cell in self.cellList:
self.assign_cell_region(cell)
self.grow_cell(cell)
# mitosis_list=self.make_mitosis_list()
# self.perform_mitosis(mitosis_list)
def perform_mitosis(self, mitosis_list):
for cell in mitosis_list:
if self.mitosisVisualizationFlag:
self.visualizeMitosis(cell) # change cell type to "Mitosing"
### Choose whether cell will divide along AP or random orientation
AP_divide = random()
if AP_divide <= self.fraction_AP_oriented:
self.divideCellOrientationVectorBased(cell, 0, 1, 0)
else:
self.divideCellRandomOrientation(cell)
if self.mitosisVisualizationFlag:
self.mitosisVisualizationCountdown(
) # Maintains cell type as "Mitosing" for a set window of time (self.mitosisVisualizationWindow)
# UpdateAttributes is inherited from MitosisSteppableBase
# and it is called automatically by the divideCell() function
# It sets the attributes of the parent and daughter cells:
def updateAttributes(self):
parentCell = self.mitosisSteppable.parentCell
childCell = self.mitosisSteppable.childCell
childCell.targetVolume = childCell.volume
childCell.lambdaVolume = parentCell.lambdaVolume
childCell.targetSurface = childCell.surface
childCell.lambdaSurface = parentCell.lambdaSurface
parentCell.targetVolume = parentCell.volume
parentCell.targetSurface = parentCell.surface
childCell.type = parentCell.type
parentDict = CompuCell.getPyAttrib(parentCell)
childDict = CompuCell.getPyAttrib(childCell)
### Make a copy of the parent cell's dictionary and attach to child cell
for key, item in parentDict.items():
childDict[key] = deepcopy(parentDict[key])
def assign_cell_region(self, cell):
cellDict = CompuCell.getPyAttrib(cell)
yCM = cell.yCM / float(cell.volume)
if yCM > self.y_EN_ant: # if cell is anterior to EN stripes
cellDict["region"] = 0
# if (cell.type!=4 and cell.type!=2): # if cell is not En or mitosing
# cell.type=1 # AnteriorLobe
elif yCM > self.y_EN_pos: # if cell is in EN-striped region
cellDict["region"] = 1
if (cell.type != 2
and cell.type != 4): # if cell is not En or mitosing
cell.type = 5 # Segmented
elif yCM > self.y_GZ_border: # if cell is in anterior region of GZ
cellDict["region"] = 2
if (cell.type != 2
and cell.type != 4): # if cell is not En or mitosing
cell.type = 3 #GZ
else: # if cell is in posterior region of GZ
cellDict["region"] = 3
if cell.type != 4: #if cell is not mitosing
cell.type = 3 # GZ
def initiate_cell_volume(self, cell):
phase = random(
) # chooses a phase between 0 and 1 to initialize cell volume
volume_difference = self.Vmin_divide - cell.volume
new_volume = phase * volume_difference + cell.volume
cell.targetVolume = new_volume
def attach_growth_timer(self, cell):
phase = random(
) # picks a random phase between 0 and 1 to initialize cell growth timer
growth_timer = phase
return growth_timer
def grow_cell(self, cell):
cellDict = CompuCell.getPyAttrib(cell)
region = cellDict["region"]
r_grow = self.r_grow_list[region]
if cellDict["growth_timer"] >= 1:
if cell.targetVolume <= self.Vmax:
cell.targetVolume += int(cellDict["growth_timer"])
cellDict["growth_timer"] = 0
else:
cellDict["growth_timer"] += r_grow
def make_mitosis_list(self):
mitosis_list = []
for cell in self.cellList:
cellDict = CompuCell.getPyAttrib(cell)
region = cellDict["region"]
mitosis_probability = self.r_mitosis_list[region] / self.window
if mitosis_probability >= random():
if cell.volume >= self.Vmin_divide:
mitosis_list.append(cell)
return mitosis_list
def find_posterior_EN_stripe(self):
y_EN_pos = 9999
for cell in self.cellList:
if cell.type == 2: # EN cell
yCM = cell.yCM / float(cell.volume)
if yCM < y_EN_pos:
y_EN_pos = yCM
return y_EN_pos
def find_anterior_EN_stripe(self):
y_EN_ant = 0
for cell in self.cellList:
if cell.type == 2: # EN cell
yCM = cell.yCM / float(cell.volume)
if yCM > y_EN_ant:
y_EN_ant = yCM
return y_EN_ant
def find_y_GZ_mitosis_border(self):
y_GZ_pos = self.find_posterior_GZ()
y_GZ_border = y_GZ_pos + self.y_GZ_mitosis_border_percent * (
self.y_EN_pos - y_GZ_pos)
return y_GZ_border
def find_posterior_GZ(self):
y_GZ_pos = 9999
for cell in self.cellList:
yCM = cell.yCM / float(cell.volume)
if yCM < y_GZ_pos:
y_GZ_pos = yCM
return y_GZ_pos
# def calculate_t_grow(self,r_mitosis):
# if r_mitosis > 0:
# t_cycle=self.window/r_mitosis # approx time to double volume, in MCS
# t_grow=2*t_cycle/self.V_divide # MCS per pixel growth
# else:
# t_grow=999999999
# return t_grow
def visualizeMitosis(self, cell):
cellDict = CompuCell.getPyAttrib(cell)
cellDict['mitosisVisualizationTimer'] = self.mitosisVisualizationWindow
cellDict['returnToCellType'] = cell.type
cell.type = 4 # set to mitosing cell
def mitosisVisualizationCountdown(self):
for cell in self.cellList:
if cell.type == 4: # if Mitosis cell
cellDict = CompuCell.getPyAttrib(cell)
if cellDict['mitosisVisualizationTimer'] <= 0:
cell.type = cellDict['returnToCellType']
else:
cellDict['mitosisVisualizationTimer'] -= 1
