avimanyu786
commented
4 years ago Apparently, if you keep the position of the initial cell at (0,0,0.5) and raise the default number of maximum cells to 20000, you can simulate cells in 2D quite conveniently, over ~12000 cells. I just tested this on a GeForce GTX 1050 Ti with 4GB video memory.
Please try experimenting with the following code(worked for the above screenshots):
import random
from CellModeller.Regulation.ModuleRegulator import ModuleRegulator
from CellModeller.Biophysics.BacterialModels.CLBacterium import CLBacterium
from CellModeller.GUI import Renderers
import numpy
import math
def setup(sim):
# Set biophysics, signalling, and regulation models
biophys = CLBacterium(sim, jitter_z=False, gamma = 20, max_planes=1, max_cells=20000)
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), dir=(1,0,0))
# Add some objects to draw the models
therenderer = Renderers.GLBacteriumRenderer(sim)
sim.addRenderer(therenderer)
sim.pickleSteps = 20
def init(cell):
# Specify mean and distribution of initial cell size
cell.targetVol = 3.0 + random.uniform(0.0,0.5)
# Specify growth rate of cells
cell.growthRate = 1.0
cell.color = (0.0,1.0,0.0)
def update(cells):
#Iterate through each cell and flag cells that reach target size for division
for (id, cell) in cells.items():
if cell.volume > cell.targetVol:
cell.divideFlag = True
def divide(parent, d1, d2):
# Specify target cell size that triggers cell division
d1.targetVol = 3.0 + random.uniform(0.0,0.5)
d2.targetVol = 3.0 + random.uniform(0.0,0.5)It's a modified version of Tutorial_1c.py. I've kept only the base plane and reduced max_planes to 1. Hope that helps.
odanieloliveira
timrudge
danieljones333
Dear all, I've recently started to use CellModeller for my Master's thesis project. I was able to install the master branch following Tim Rudge's instructions posted in the comment section of another issue. However, when trying to run Tutorial1a as well as my own models the cells are leaving the plane (growing in 3D) even though I have set jitter_z=False. Does anybody have the same issue and if so, is there any way to fix this?
Thanks in advance for your help and time. Best regards, Daniel