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)
sig = GridDiffusion(sim, n_signals, grid_dim, grid_size, grid_orig, [1.0, 1.0])
integ = CLCrankNicIntegrator(sim, n_signals, n_species, max_cells, sig)
# 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=(-3.0,0,0)) #Add
sim.addCell(cellType=1, pos=(3.0,0,0)) #Add
# 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 = 20
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, \
max_substeps=8, \
max_cells=max_cells, \
max_contacts=32, \
max_sqs=192**2, \
jitter_z=False, \
reg_param=2, \
gamma=10)
# 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)
'''
biophys = CLFixedPosition(sim, max_cells=max_cells)
sig = GridDiffusion(sim, 1, grid_dim, grid_size, grid_orig, [10.0])
integ = CLCrankNicIntegrator(sim, 1, 1, max_cells, sig, boundcond='mirror')
# 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