def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, \
max_cells=max_cells, \
max_contacts=32, \
max_sqs=128**2, \
jitter_z=False, \
reg_param=2, \
gamma=10)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-4)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#load data from pickle file
dataFileName = '' # Edit to include your filename here
# Or pop up a dialog to choose a pickle
if dataFileName=='':
print "Please edit the model file to specify a pickle file."
print " -- No data was loaded and there are no cells in this simulation!"
else:
# Import the data and load into Simulator
print "Loading data from pickle file: %s"%(dataFileName)
import cPickle
data = cPickle.load(open(dataFileName,'r'))
sim.loadFromPickle(data)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
#integ = ScipyODEIntegrator(sim, 1, 4, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig, boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64*64, jitter_z=True, reg_param=2, gamma=5.0)
biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
biophys.addPlane((0,0,0.5), (0,0,-1), 5e-4)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
#for i in range(4):
# for j in range(4):
# sim.addCell(cellType=0, pos=(i*16-32,j*16-32,0))
# sim.addCell(cellType=1, pos=(i*16-32-8,j*16-32-8,0))
sim.addCell(cellType=1, pos=(-20.0,0,0), len=2.0)
sim.addCell(cellType=0, pos=(20.0,0,0), len=2.0)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False, max_planes=9)
sim.dt = 0.025
#biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
#biophys.addPlane((0,0,0.5), (0,0,-1), math.sqrt(7.5e-4))
angs = [i*math.pi/4 for i in range(8)]
for a in angs:
x = math.cos(a)
y = math.sin(a)
p = (50*x,50*y,0)
n = (-x,-y,0)
biophys.addPlane(p,n, 1.0)
regul = ModuleRegulator(sim) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#ct = 0
#for x in range(-4,5):
# for y in range(-4,5):
sim.addCell(cellType=0, pos=(0,-10,0), color=(1,0,0)) #x*40,y*40,0))
sim.addCell(cellType=1, pos=(0,10,0), color=(0,0,1)) #x*40,y*40,0))
# ct += 1
#sim.addCell(cellType=1, pos=(20,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 1
def setup(sim):
# Set biophysics, signalling, and regulation models
#
biophys = CLBacterium(sim,
jitter_z=True,
periodic=True,
N_x=3,
N_y=3,
max_cells=2**11,
max_contacts=16)
# add some planes to coral cells
planeWeight = 1.0
#biophys.addPlane((0,0,0), (+1,0,0), planeWeight) # left side
#biophys.addPlane((0,0,0), (0,+1,0), planeWeight) # front side
#biophys.addPlane((15.0, 0, 0), (-1,0,0), planeWeight) # right side
#biophys.addPlane((0, 15.0, 0), (0,-1,0), planeWeight) # rear side
biophys.addPlane((0, 0, 0), (0, 0, +1), planeWeight) # base
# use this file for reg too
regul = ModuleRegulator(sim)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(5, 7.5, 0))
sim.addCell(cellType=1, pos=(10, 7.5, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 3, max_cells, sig, boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(-10.0,0,0)) #Add
sim.addCell(cellType=1, pos=(10.0,0,0)) #Add
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 1, max_cells, sig, boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_planes=9)
sim.dt = 0.025
#biophys.addPlane((0,0,-0.5), (0,0,1), 1.0)
#biophys.addPlane((0,0,0.5), (0,0,-1), math.sqrt(7.5e-4))
'''
angs = [i*math.pi/8 for i in range(8)]
for a in angs:
x = math.cos(a)
y = math.sin(a)
p = (30*x,30*y,0)
n = (-x,-y,0)
biophys.addPlane(p,n, 1.0)
'''
biophys.addPlane((0,0,0),(0,0,-1),1.0)
regul = ModuleRegulator(sim) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#ct = 0
#for x in range(-4,5):
# for y in range(-4,5):
sim.addCell(cellType=0, pos=(0,0,-5), color=(1,1,1)) #x*40,y*40,0))
# ct += 1
#sim.addCell(cellType=1, pos=(20,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
dim = (32,32,4)
size = (5,5,5)
orig = (-0.5*(dim[0]-1)*size[0],-0.5*(dim[1]-1)*size[1],-0.5*(dim[2]-1)*size[2])
# Set biophysics, signalling, and regulation models
sig = GridDiffusion(sim, 2, dim, size, orig, [1e-1,1e-1], [1.0,1.0])
#integ = ScipyODEIntegrator(sim, 0, 3, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 2, 3, max_cells, sig)
#integ = CrankNicIntegrator(sim, 2, 3, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.75)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-2)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
sim.init(biophys, regul, sig, integ)
sim.addCell(cellType=0, pos=(-20,1,0))
sim.addCell(cellType=1, pos=(20,0,1))
# Add some objects to draw the models
sigrenderer = Renderers.GLGridRenderer(sig, integ)
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrenderer)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, \
max_cells=max_cells, \
max_contacts=32, \
max_sqs=128**2, \
jitter_z=False, \
reg_param=2, \
gamma=10)
biophys.addPlane((0, 0, -0.5), (0, 0, 1), 0.2)
biophys.addPlane((0, 0, 0.5), (0, 0, -1), 1e-4)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#load data from pickle file
dataFileName = '' # Edit to include your filename here
# Or pop up a dialog to choose a pickle
if dataFileName == '':
print "Please edit the model file to specify a pickle file."
print " -- No data was loaded and there are no cells in this simulation!"
else:
# Import the data and load into Simulator
print "Loading data from pickle file: %s" % (dataFileName)
import cPickle
data = cPickle.load(open(dataFileName, 'r'))
sim.loadFromPickle(data)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False)
# add the planes to set physical boundaries of cell growth
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
# Here we set up the numerical integration:
# Crank-Nicholson method:
#integ = CLCrankNicIntegrator(sim, 1, 2, max_cells, sig, boundcond='reflect')
# Alternative is to use the simple forward Euler method:
integ = CLEulerSigIntegrator(sim, 1, 2, max_cells, sig, boundcond='reflect')
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, sig, integ)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sigrend = Renderers.GLGridRenderer(sig, integ) # Add
sim.addRenderer(sigrend) #Add
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(
sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=50**2,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=10.0)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
#biophys.addPlane((0,0,-radiusD/2.0), (0,0,+1), planeWeight) # front of box
#biophys.addPlane((0,0,+radiusD/2.0), (0,0,-1), planeWeight) # back of box
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
solverParams = None
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# initialise 2 cells with different lengths, radii
sim.addCell(
cellType=0,
len=lengthD,
rad=radiusD,
pos=(+init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
sim.addCell(
cellType=1,
len=lengthD,
rad=radiusD,
pos=(-init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True, gamma=10, max_planes=6)
biophys.addPlane((0, 0, 0), (0, 0, 1), 1.0) #Base plane
biophys.addPlane((10, 0, 0), (-1, 0, 0), 1.0)
biophys.addPlane((-10, 0, 0), (1, 0, 0), 1.0)
biophys.addPlane((0, 10, 0), (0, -1, 0), 1.0)
biophys.addPlane((0, -10, 0), (0, 1, 0), 1.0)
biophys.addPlane((0, 0, 10), (0, 0, -1), 1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(-5, -1, 0.5), dir=(-1, 0, 0), rad=0.4)
sim.addCell(cellType=0, pos=(6, 8, 0.5), dir=(-0.5, 0.2, 0), rad=0.4)
sim.addCell(cellType=0, pos=(-1, -7, 1), dir=(0, 0, 0), rad=0.4)
#sim.addCell(cellType=0, pos=(1,11,0.5), dir=(1,0.4,0), rad=0.4)
#sim.addCell(cellType=0, pos=(-1,7,0.5), dir=(1,1,0), rad=0.4)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=50**2,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=10.0)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
#biophys.addPlane((0,0,-radiusD/2.0), (0,0,+1), planeWeight) # front of box
#biophys.addPlane((0,0,+radiusD/2.0), (0,0,-1), planeWeight) # back of box
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
solverParams = None
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# initialise 2 cells with different lengths, radii
sim.addCell(cellType=0,
len=lengthD,
rad=radiusD,
pos=(+init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
sim.addCell(cellType=1,
len=lengthD,
rad=radiusD,
pos=(-init_sep / 2.0, radiusD, 0),
dir=(1, 0, 0))
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [1.0])
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=64**2, jitter_z=False, reg_param=2)
biophys.addPlane((0,-16,0),(0,1,0),0.2)
biophys.addPlane((0,16,0),(0,-1,0),0.2)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GL2DBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.addCell(pos=(0,0,0), len=2.0)
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0], initLevels=[5e-3])
#integ = ScipyODEIntegrator(sim, 1, 4, max_cells, sig, True)
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig)
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=32**2, jitter_z=True, reg_param=2)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-3)
reg = ModuleRegulator(sim, __file__)
sim.init(biophys, reg, sig, integ)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.addCell(cellType=0, pos=(0,0,0))
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
sim.addCell(cellType=0, pos=(0,0,0))
biophys.addPlane((0,0,0),(0,0,-1),1.0)
biophys.addPlane((0,0,0),(0,0,1),5e-2)
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 5, max_cells, sig, boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
biophys.addPlane((0,-16,0), (0,1,0), 1)
biophys.addPlane((0,16,0), (0,-1,0), 1)
reg = ModuleRegulator(sim)
sim.init(biophys, reg, sig, integ)
sim.addCell(cellType=1, pos=(-20.0,0,0), len=2.0)
sim.addCell(cellType=0, pos=(20.0,0,0), len=2.0)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True)
regul = ModuleRegulator(sim, sim.moduleName) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
sim.addCell(cellType=0, pos=(0, 0, 0))
biophys.addPlane((0, 0, 0), (0, 0, -1), 1.0)
biophys.addPlane((0, 0, 0), (0, 0, 1), 5e-2)
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, max_cells=max_cells, max_contacts=32, max_sqs=128**2, jitter_z=False, reg_param=2, gamma=10)
biophys.addPlane((0,0,-0.5), (0,0,1), 0.2)
biophys.addPlane((0,0,0.5), (0,0,-1), 1e-4)
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# Only biophys and regulation
sim.init(biophys, regul, None, None)
#sim.addCell(cellType=0, pos=(0,0,0))
#load data from pickle file
import cPickle
data = cPickle.load(open('data/BiofilmWallLessCrash_no_alternation_9-12-56-25-09-12/step-00700.pickle','r'))
cellStates = data[0]
print "Loading %i cells"%len(cellStates)
sim.cellStates = cellStates
regul.cellStates = cellStates
biophys.load_from_cellstates(cellStates)
idx_map = {}
for id,state in sim.cellStates.iteritems():
idx_map[state.id] = state.idx
sim.idToIdx = idx_map
# parents = data[1]
# for id,state in sim.cellStates.iteritems():
# p = lineage(parents, [1,2], id)
# if p == 1: state.color = [0, 1, 0]
# elif p == 2: state.color = [0, 0, 1]
#import numpy.random
#cellcols = numpy.random.uniform(0,1,81*3)
#cellcols.shape = (81,3)
#for id,state in sim.cellStates.iteritems():
# state.color = list(cellcols[state.cellType,:])
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(
sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=Num_x * Num_y,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=meshParam,
L_x=Len_x,
L_y=Len_y,
)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
# what happens if we add some sides?
biophys.addPlane((0, 0, 0), (+1, 0, 0), planeWeight) # left side
biophys.addPlane((Len_x, 0, 0), (-1, 0, 0), planeWeight) # right side
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
""" CASE 1 - HIGH NUTRIENTS """
solverParams = dict(
h=0.5 * meshParam,
origin=[0.0, 0.0, 0.0],
N_x=2 * Num_x,
L_x=Len_x,
u0=1.0,
K=0.0033,
mu_eff=0.001,
pickleSteps=10,
rel_tol=1e-6,
mesh_type="crossed",
delta=40.0,
)
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# randomly initialise a line of cells along the bottom
RandomSeedOnLine(sim, Len_x, num_initial_cells, initialVola, initialVola, radius)
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
# sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim,
jitter_z=True,
gamma=20,
max_planes=5,
max_cells=500000)
biophys.addPlane((0, 0, 0), (0, 0, 1), 1.0) #base plane
biophys.addPlane((gridsize / 2, 0, 0), (-1, 0, 0), 1.0)
biophys.addPlane((-gridsize / 2, 0, 0), (1, 0, 0), 1.0)
biophys.addPlane((0, gridsize / 2, 0), (0, -1, 0), 1.0)
biophys.addPlane((0, -gridsize / 2, 0), (0, 1, 0), 1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addPillars(dist, gridsize, rad)
sim.addLawn(gridsize, cell_lens, 1.1)
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def setup(sim):
# Set biophysics, signalling, and regulation models
#
biophys = CLBacterium(sim,
jitter_z=False,
periodic=True,
N_x=3,
N_y=3,
max_cells=8,
max_contacts=12)
# add some planes to make the system 1-D
planeWeight = 1.0
biophys.addPlane((0, 7.0, 0), (0, +1, 0),
planeWeight) # bottom channel boundary
biophys.addPlane((0, 8.0, 0), (0, -1, 0),
planeWeight) # top channel boundary
# temporarily add some planes to stop cells leaving the domain
#biophys.addPlane((0, 0, 0), (+1,0,0), planeWeight) # left channel boundary
#biophys.addPlane((15.0, 0, 0), (-1,0,0), planeWeight) # right channel boundary
# use this file for reg too
regul = ModuleRegulator(sim)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(5, 7.5, 0))
sim.addCell(cellType=1, pos=(10, 7.5, 0))
if sim.is_gui:
# Add some objects to draw the models
from CellModeller.GUI import Renderers
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 10
def setup(sim):
biophys = CLBacterium(sim, jitter_z=False, gamma=10, max_planes=3) #gamme is how the external pressure makes them stop growing (high means they keep growing)
# Set certin planes that limit the simulation
biophys.addPlane( (0, 0, 0), (0, 1, 0), 1.0)
biophys.addPlane( (-8, 0, 0), (1, 0, 0), 1.0)
biophys.addPlane( (8, 0, 0), (-1, 0, 0), 1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-7.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-6.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-5.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-4.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-3.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-2.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-1.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(-0.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(0.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(1.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(2.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(3.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(4.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(5.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(6.5,2,0), dir=(0,1,0))
sim.addCell(cellType=int(random.getrandbits(1)), pos=(7.5,2,0), dir=(0,1,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def setup(sim):
# Set biophysics, signalling, and regulation models. Add dolfin solver if used.
biophys = CLBacterium(sim,
max_substeps=8,
max_cells=max_cells,
max_contacts=32,
max_sqs=Num_x * Num_y,
jitter_z=False,
reg_param=0.04,
gamma=500,
periodic=False,
grid_spacing=meshParam,
L_x=Len_x,
L_y=Len_y)
# add mechanical planes
planeWeight = 1.0
biophys.addPlane((0, 0, 0), (0, 1, 0), planeWeight) # base of box
# what happens if we add some sides?
biophys.addPlane((0, 0, 0), (+1, 0, 0), planeWeight) # left side
biophys.addPlane((Len_x, 0, 0), (-1, 0, 0), planeWeight) # right side
regul = ModuleRegulator(sim, __file__) # use this file for reg too
# compile a list of solver parameters (using scaled values)
""" CASE 1 - HIGH NUTRIENTS """
solverParams = dict(h=0.5 * meshParam,
origin=[0.0, 0.0, 0.0],
N_x=2 * Num_x,
L_x=Len_x,
u0=1.0,
K=0.0033,
mu_eff=0.001,
pickleSteps=10,
rel_tol=1e-6,
mesh_type='crossed',
delta=40.0)
# add biophysics, regulation, [solver], objects to simulator
sim.init(biophys, regul, None, None, solverParams)
# randomly initialise a line of cells along the bottom
RandomSeedOnLine(sim, Len_x, num_initial_cells, initialVola, initialVola,
radius)
# Add some objects to draw the models
mainRenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(mainRenderer)
# How often should we output data?
sim.renderEveryNSteps = 1
#sim.savePickle = True
sim.pickleSteps = saveEvery
print "Ready."
def setup(sim):
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim,
1,
5,
max_cells,
sig,
boundcond='reflect')
biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
biophys.addPlane((0, -16, 0), (0, 1, 0), 1)
biophys.addPlane((0, 16, 0), (0, -1, 0), 1)
reg = ModuleRegulator(sim)
sim.init(biophys, reg, sig, integ)
sim.addCell(cellType=1, pos=(-20.0, 0, 0), len=2.0)
sim.addCell(cellType=0, pos=(20.0, 0, 0), len=2.0)
sigrend = Renderers.GLGridRenderer(sig, integ)
therend = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(sigrend)
sim.addRenderer(therend)
sim.pickleSteps = 10
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=True, gamma = 20, max_planes=5)
biophys.addPlane((0,0,0),(0,0,1),1.0) #Base plane
biophys.addPlane((10,0,0),(-1,0,0),1.0)
biophys.addPlane((-10,0,0),(1,0,0),1.0)
biophys.addPlane((0,10,0),(0,-1,0),1.0)
biophys.addPlane((0,-10,0),(0,1,0),1.0)
# use this file for reg too
regul = ModuleRegulator(sim, sim.moduleName)
# Only biophys and regulation
sim.init(biophys, regul, None, None)
# Specify the initial cell and its location in the simulation
sim.addCell(cellType=0, pos=(0,0,0.5))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
