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