new_contents: import ode
   
   
  def inducer_AHL(t, y):
      degradation = 0 * y[0]
      return 0.0 - degradation
           
   
  def mRNA_pTetR(t, y):
      production = 0.062233 #Vmax
      degradation = 0.0058 * y[1]
      return production - degradation
           
   
  def peptide_RBS1(t, y):
      production = 0.595 * y[1]
      degradation = 0.00116 * y[2]
      return production - degradation
   
   
  def mRNA_pLasR(t, y):
      production = 0.0 + ((6.817e-08*(y[5]**2))/(7.702e-05**2 + y[5]**2))
      degradation = 0.0058 * y[3]
      return production - degradation
           
   
  def peptide_RBS2(t, y):
      production = 0.1785 * y[3]
      degradation = 0.0061 * y[4]
      return production - degradation
           
   
  def interaction_LasR_AHL(t, y):
      association = 16000 * y[0] * y[2]
      dissociation = 0 * y[5]
      return association - dissociation
    
  circuitODE = range(6)
  y = range(6)        
  circuitODE[0] = inducer_AHL
  circuitODE[1] = mRNA_pTetR
  circuitODE[2] = peptide_RBS1
  circuitODE[3] = mRNA_pLasR
  circuitODE[4] = peptide_RBS2
  circuitODE[5] = interaction_LasR_AHL
  y[0] = 1e-09    # [inducer_AHL]
  y[1] = 1e-06    # [mRNA_pTetR]
  y[2] = 1e-06    # [peptide_RBS1]
  y[3] = 0.0    # [mRNA_pLasR]
  y[4] = 0.0    # [peptide_RBS2]
  y[5] = 0.0    # [interaction_LasR_AHL]
   
   
  t0 = 0.0
  tmax = 1800.0
  dt = 0.1
  outfile = 'lasR_system.csv'
  f = open(outfile, 'w')
  header = ['time', 'AHL', 'LasR_mRNA', 'LasR', 'GFP_mRNA', 'GFP', 'LasR.AHL']
  f.write(','.join(header) + '\n')
  for x in ode.multirk4(circuitODE, t0, y, dt, tmax):
      f.write(','.join([str(item) for item in x]) + '\n')
  f.close()
   
   
  t0 = 0.0
  tmax = 600.0
  dt = 0.1
  for x in ode.multirk4(circuitODE, t0, y, dt, tmax):
      print ','.join([str(item) for item in x])
   
  ''' Corresponding SciPy version
  from scipy.integrate import odeint
  from numpy import linspace, array
   
  def geneticCircuit(y, t):
      return(0.0 - (0*y[0]),
             0.062233 - (0.0058*y[1]),
             (0.595*y[1]) - (0.00116*y[2]),
             (0.0+((6.817e-08*(y[5]**2))/(7.702e-05**2+y[5]**2))) - (0.0058*y[3]),
             (0.1785*y[3]) - (0.0061*y[4]),
             (16000*y[0]*y[2]) - (0*y[5]))
   
  yinit = array([1e-09, 1e-06, 1e-06, 0.0, 0.0, 0.0])
  time = linspace(0.0, 2000.0, 20000)
  y = odeint(geneticCircuit, yinit, time)
  '''
  
subject: Create LasR.AHL.py