Tutorial_2a.py

import random
from CellModeller.Regulation.ModuleRegulator import ModuleRegulator
from CellModeller.Biophysics.BacterialModels.CLBacterium import CLBacterium
from CellModeller.GUI import Renderers
import numpy
import math

#Import Euler integrator for solving ODE system of chemical species inside the cells
from CellModeller.Integration.CLEulerIntegrator import CLEulerIntegrator

max_cells = 100000


def setup(sim):
    # Set biophysics, signalling, and regulation models
    biophys = CLBacterium(sim, max_cells=max_cells, jitter_z=False)
    integ = CLEulerIntegrator(sim, 1, max_cells)

    # use this file for reg too
    regul = ModuleRegulator(sim)
    # Only biophys and regulation
    sim.init(biophys, regul, None, 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)

    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
    # Specify initial concentration of chemical species
    cell.species[:] = [0]


def specRateCL():
    return '''
    const float k1 = 2.f;
    float x0 = species[0];
    rates[0] = k1;
    '''
    # k1 = production rate of x0


def update(cells):
    #Iterate through each cell and flag cells that reach target size for division
    for (id, cell) in cells.items():
        cell.color = [numpy.clip(cell.species[0]/6.0,0.0,1.0), 1.0, 0.1]
        if cell.volume > cell.targetVol:
            a = 1
            cell.asymm = [a,1]
            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)