Team:Bordeaux/SourceCodeModelling

From 2012.igem.org

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<div class="grid9">
<div class="grid9">
<h2>iGEM - Bordeaux - Source Code</h2>
<h2>iGEM - Bordeaux - Source Code</h2>
 +
<p>
 +
<h4>Init_PEB.py file</h4>
                                                 <pre class="prettyprint lang-py">
                                                 <pre class="prettyprint lang-py">
 +
r"""
 +
File contains var
 +
"""
 +
 +
__projet__ = 'iGEM '
 +
__author__ = 'Djemiel Christophe, Freche Arnaud'
 +
__copyright__ = 'Copyright (c) 2012 BordeauxTeam'
 +
__license__ = ''
 +
__vcs_id__ = '$Id$'
 +
__version__ = '1.0'
 +
 +
#var
 +
directory_pictures="pictures_simulation/"
 +
 +
#initial parameters
 +
nb_bacteria=8000
 +
 +
#features constitutive
 +
seuil_acivation_recepteur1=0.75
 +
seuil_acivation_recepteur2=0.75
 +
seuil_acivation_recepteur3=0.75
 +
 +
#mutation
 +
seuil_mutation_operon=0.05
 +
seuil_mutation_LasR=0.05
 +
seuil_mutation_LuxS=0.05
 +
seuil_mutation_BetaGal=0.05
 +
seuil_mutation_LuxBox=0.05
 +
seuil_mutation_LuxI=0.05
 +
seuil_mutation_MCherry=0.05
 +
seuil_mutation_QBox=0.05
 +
seuil_mutation_LasI=0.05
 +
 +
#change state
 +
seuil_etat1_2=0.05
 +
 +
#noise
 +
noise_pourcent=0.0001
 +
seuil_bruit1=0.33
 +
seuil_bruit2=0.66
 +
 +
#stimulus light
 +
seuil_transfo_lumiere=0.7
 +
diameter_light=1
 +
 +
rayon_action=0.075
 +
 +
                                                </pre>
 +
</p>
 +
 +
<p>
 +
<h4>PEP.py file</h4>
 +
 +
                                                <pre class="prettyprint lang-py">
 +
#!/usr/bin/python
 +
# -*- coding: iso-8859-1 -*-
 +
 +
 +
import random
 +
from pylab import *
 +
from numpy import *
 +
from init_PEB import *
 +
import os
 +
 +
 +
list_bacteria = []
 +
lxw=[]
 +
lyw=[]
 +
lxb=[]
 +
lyb=[]
 +
lxr=[]
 +
lyr=[]
 +
lxg=[]
 +
lyg=[]
 +
lxn=[]
 +
lyn=[]
 +
 +
 +
def features_bacteria ():
 +
r"""
 +
Function attribute all features at the bacteria
 +
"""
 +
#Coordinates
 +
x=random.uniform(0,10) # position x of the bacteria on the petri dish
 +
List[0]=x
 +
y=random.uniform(0,10) # position x of the bacteria on the petri dish
 +
List[1]=y
 +
 +
#States
 +
state1=None
 +
List[2]=state1
 +
state2=None
 +
List[3]=state2
 +
state3=None
 +
List[4]=state3
 +
 +
#Operon 1
 +
LasR_box=None
 +
List[5]=LasR_box
 +
LuxS=None
 +
List[6]=LuxS
 +
Beta_gal=None
 +
List[7]=Beta_gal
 +
 +
#Operon 2
 +
Lux_box=None
 +
List[8]=Lux_box
 +
LuxI=None
 +
List[9]=LuxI
 +
m_cherry=None
 +
List[10]=m_cherry
 +
 +
#Operon 3
 +
Q_box=None
 +
List[11]=Q_box
 +
LasI=None
 +
List[12]=LasI
 +
GFP=None
 +
List[13]=GFP
 +
 +
#Operon constitutive
 +
recepteur1=None
 +
List[14]=recepteur1
 +
recepteur2=None
 +
List[15]=recepteur2
 +
recepteur3=None
 +
List[16]=recepteur3
 +
 +
return List
 +
 +
 +
 +
def feature_constitutive():
 +
 +
for j in range (0,len(list_bacteria)):
 +
proba_active_14=random.uniform(0,1)
 +
proba_active_15=random.uniform(0,1)
 +
proba_active_16=random.uniform(0,1)
 +
 +
if proba_active_14<=seuil_acivation_recepteur1:
 +
list_bacteria[j][14]=1
 +
else:
 +
list_bacteria[j][14]=0
 +
 +
if proba_active_15<=seuil_acivation_recepteur2:
 +
list_bacteria[j][15]=1
 +
else:
 +
list_bacteria[j][15]=0
 +
 +
if proba_active_16<=seuil_acivation_recepteur3:
 +
list_bacteria[j][16]=1
 +
else:
 +
list_bacteria[j][16]=0
 +
 +
def mutation():
 +
 +
for j in range (0,len(list_bacteria)):
 +
proba_mutation=random.uniform(0.1)
 +
if proba_mutation<=0.05:
 +
proba_mutation_LasR=random.uniform(0.1)
 +
proba_mutation_LuxS=random.uniform(0.1)
 +
proba_mutation_BetaGal=random.uniform(0.1)
 +
proba_mutation_LuxBox=random.uniform(0.1)
 +
proba_mutation_LuxI=random.uniform(0.1)
 +
proba_mutation_MCherry=random.uniform(0.1)
 +
proba_mutation_QBox=random.uniform(0.1)
 +
proba_mutation_LasI=random.uniform(0.1)
 +
proba_mutation_GFP=random.uniform(0.1)
 +
if proba_mutation_LasR<=seuil_mutation_LasR:
 +
list_bacteria[j][5]=0
 +
if proba_mutation_LuxS<=seuil_mutation_LuxS:
 +
list_bacteria[j][6]=0
 +
if proba_mutation_BetaGal<=seuil_mutation_BetaGal:
 +
list_bacteria[j][7]=0
 +
if proba_mutation_LuxBox<=seuil_mutation_LuxBox:
 +
list_bacteria[j][8]=0
 +
if proba_mutation_LuxI<=seuil_mutation_LuxI:
 +
list_bacteria[j][9]=0
 +
if proba_mutation_MCherry<=seuil_mutation_MCherry:
 +
list_bacteria[j][10]=0
 +
if proba_mutation_QBox<=seuil_mutation_QBox:
 +
list_bacteria[j][11]=0
 +
if proba_mutation_LasI<=seuil_mutation_LasI:
 +
list_bacteria[j][12]=0
 +
if proba_mutation_GFP<=seuil_mutation_GFP:
 +
list_bacteria[j][13]=0
 +
 +
 +
def active_state():
 +
r"""
 +
Function permit to active the state of the bacteria according the activation of these genes
 +
"""
 +
for j in range (0,len(list_bacteria)):
 +
#State 1
 +
if list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][7]==1:
 +
list_bacteria[j][2]=1
 +
list_bacteria[j][3]=0
 +
list_bacteria[j][4]=0
 +
 +
#State 2
 +
if list_bacteria[j][8]==1 and list_bacteria[j][9]==1 and list_bacteria[j][10]==1:
 +
list_bacteria[j][2]=0
 +
list_bacteria[j][3]=1
 +
list_bacteria[j][4]=0
 +
 +
#State 3
 +
if list_bacteria[j][11]==1 and list_bacteria[j][12]==1 and list_bacteria[j][13]==1:
 +
list_bacteria[j][2]=0
 +
list_bacteria[j][3]=0
 +
list_bacteria[j][4]=1
 +
 +
def change_state():
 +
r"""
 +
Function permit to the bacteria changing state
 +
"""
 +
for j in range (0,len(list_bacteria)):
 +
# State 1 --> State 2
 +
if  list_bacteria[j][2]==1 and list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][14]==1:
 +
proba=random.uniform(0,1)
 +
if proba<=seuil_etat1_2:
 +
list_bacteria[j][8] =1
 +
list_bacteria[j][9] =1
 +
list_bacteria[j][10] =1
 +
 +
def noise(noise_pourcent):
 +
r"""
 +
Create a noise before the first stimulation light. Take one argument : noise_pourcent = the noise that we want
 +
"""
 +
for j in range (0,len(list_bacteria)):
 +
proba=random.uniform(0,1)
 +
if proba<=noise_pourcent:
 +
proba2=random.uniform(0,1)
 +
if 0<=proba2<seuil_bruit1:
 +
list_bacteria[j][5]=1
 +
list_bacteria[j][6]=1
 +
list_bacteria[j][7]=1
 +
if seuil_bruit1<=proba2<seuil_bruit2:
 +
list_bacteria[j][8]=1
 +
list_bacteria[j][9]=1
 +
list_bacteria[j][10]=1
 +
if seuil_bruit2<=proba2<1:
 +
list_bacteria[j][11]=1
 +
list_bacteria[j][12]=1
 +
list_bacteria[j][13]=1
 +
 +
 +
def stimulus_light():
 +
r"""
 +
Function create the first stimulation light
 +
"""
 +
for j in range (0,len(list_bacteria)):
 +
proba_recepteur=random.uniform(0,1)
 +
if ((list_bacteria[j][0]-5)*(list_bacteria[j][0]-5))+((list_bacteria[j][1]-5)*(list_bacteria[j][1]-5))<=diameter_light and list_bacteria[j][5]!=0  and list_bacteria[j][6]!=0  and list_bacteria[j][7]!=0:
 +
proba=random.uniform(0,1)
 +
if proba<=seuil_transfo_lumiere:
 +
list_bacteria[j][5]=1
 +
list_bacteria[j][6]=1
 +
list_bacteria[j][7]=1
 +
 +
 +
 +
def stimulus_factor(x,rayon_action):
 +
r"""
 +
Function create others stimulations
 +
"""
 +
 +
change_state()
 +
active_state()
 +
for j in range (0,len(list_bacteria)):
 +
#stimulus facteur1
 +
if list_bacteria[j][2] ==None and list_bacteria[j][3]==None and list_bacteria[j][4]==None and list_bacteria[j][14]==1 and list_bacteria[j][8]!=0  and list_bacteria[j][9]!=0  and list_bacteria[j][10]!=0:
 +
for i in range (0,len(list_bacteria)):
 +
if ((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))<=rayon_action and list_bacteria[i][2]==1 and list_bacteria[i][6]==1 :
 +
distance_voisin=((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))
 +
proba=random.uniform(0,1)
 +
if proba*distance_voisin<=x:
 +
list_bacteria[j][8] =1
 +
list_bacteria[j][9] =1
 +
list_bacteria[j][10] =1
 +
change_state()
 +
active_state()
 +
 +
for j in range (0,len(list_bacteria)):
 +
#stimulus facteur2
 +
if list_bacteria[j][2] ==None and list_bacteria[j][3]==None and list_bacteria[j][4]==None and list_bacteria[j][15]==1 and list_bacteria[j][11]!=0  and list_bacteria[j][12]!=0  and list_bacteria[j][13]!=0:
 +
for i in range (0,len(list_bacteria)):
 +
if ((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))<=rayon_action and list_bacteria[i][3]==1 and list_bacteria[i][9]==1 :
 +
distance_voisin=((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))
 +
proba=random.uniform(0,1)
 +
if proba*distance_voisin<=x:
 +
list_bacteria[j][11] =1
 +
list_bacteria[j][12] =1
 +
list_bacteria[j][13] =1
 +
change_state()
 +
active_state()
 +
 +
for j in range (0,len(list_bacteria)):
 +
#stimulus facteur2
 +
if list_bacteria[j][2] ==None and list_bacteria[j][3]==None and list_bacteria[j][4]==None and list_bacteria[j][16]==1 and list_bacteria[j][5]!=0  and list_bacteria[j][6]!=0  and list_bacteria[j][7]!=0:
 +
for i in range (0,len(list_bacteria)):
 +
if ((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))<=rayon_action and list_bacteria[i][4]==1and list_bacteria[i][12]==1 :
 +
distance_voisin=((list_bacteria[j][0]-list_bacteria[i][0])*(list_bacteria[j][0]-list_bacteria[i][0]))+((list_bacteria[j][1]-list_bacteria[i][1])*(list_bacteria[j][1]-list_bacteria[i][1]))
 +
proba=random.uniform(0,1)
 +
if proba*distance_voisin<=x:
 +
list_bacteria[j][5] =1
 +
list_bacteria[j][6] =1
 +
list_bacteria[j][7] =1
 +
change_state()
 +
active_state()
 +
 +
 +
def statistic():
 +
cpt1=0
 +
cpt2=0
 +
cpt3=0
 +
cpt4=0
 +
cpt5=0
 +
cpt6=0
 +
cpt7=0
 +
cpt8=0
 +
cpt9=0
 +
cpt10=0
 +
cpt11=0
 +
cpt12=0
 +
cpt13=0
 +
cpt14=0
 +
cpt15=0
 +
cpt16=0
 +
for j in range (0,len(list_bacteria)):
 +
if list_bacteria[j][2]==1:
 +
cpt1=cpt1+1
 +
if list_bacteria[j][3]==1:
 +
cpt2=cpt2+1
 +
if list_bacteria[j][4]==1:
 +
cpt3=cpt3+1
 +
if list_bacteria[j][5]==1:
 +
cpt4=cpt4+1
 +
if list_bacteria[j][6]==1:
 +
cpt5=cpt5+1
 +
if list_bacteria[j][7]==1 and list_bacteria[j][2]==1:
 +
cpt6=cpt6+1
 +
if list_bacteria[j][8]==1:
 +
cpt7=cpt7+1
 +
if list_bacteria[j][9]==1:
 +
cpt8=cpt8+1
 +
if list_bacteria[j][10]==1 and list_bacteria[j][3]==1:
 +
cpt9=cpt9+1
 +
if list_bacteria[j][11]==1:
 +
cpt10=cpt10+1
 +
if list_bacteria[j][12]==1:
 +
cpt11=cpt11+1
 +
if list_bacteria[j][13]==1 and list_bacteria[j][4]==1:
 +
cpt12=cpt12+1
 +
if list_bacteria[j][14]==1:
 +
cpt13=cpt13+1
 +
if list_bacteria[j][15]==1:
 +
cpt14=cpt14+1
 +
if list_bacteria[j][16]==1:
 +
cpt15=cpt15+1
 +
if list_bacteria[j][5]==1 and list_bacteria[j][7]==1 and list_bacteria[j][8]==1 and list_bacteria[j][10]==1:
 +
cpt16=cpt16+1
 +
print "\n","\n"
 +
print "OPERON A:"
 +
print "etat1=",(float(cpt1)/float(len(list_bacteria)))*100,"%"
 +
print "etat1 et etat2 à la fois=",(float(cpt16)/float(len(list_bacteria)))*100,"%"
 +
print "Las R actif=",(float(cpt4)/float(len(list_bacteria)))*100,"%"
 +
print "Production de Borat =",(float(cpt5)/float(len(list_bacteria)))*100,"%"
 +
print "Production BetaGal=",(float(cpt6)/float(len(list_bacteria)))*100,"%"
 +
print "Recepteur à PAI-1 actif=",(float(cpt15)/float(len(list_bacteria)))*100,"%","\n","\n"
 +
 +
print "OPERON B:"
 +
print "etat2=",(float(cpt2)/float(len(list_bacteria)))*100,"%"
 +
print "Lux Box fonctionnelle=",(float(cpt7)/float(len(list_bacteria)))*100,"%"
 +
print "Production de AHL=",(float(cpt8)/float(len(list_bacteria)))*100,"%"
 +
print "Production de M-Cherry=",(float(cpt9)/float(len(list_bacteria)))*100,"%"
 +
print "Recepteur à Borat actif=",(float(cpt13)/float(len(list_bacteria)))*100,"%","\n","\n"
 +
 +
 +
print "OPERON C:"
 +
print "etat3=",(float(cpt3)/float(len(list_bacteria)))*100,"%"
 +
print "Q Box fonctionnelle=",(float(cpt10)/float(len(list_bacteria)))*100,"%"
 +
print "Production de PAI-1=",(float(cpt11)/float(len(list_bacteria)))*100,"%"
 +
print "Production de GFP=",(float(cpt12)/float(len(list_bacteria)))*100,"%"
 +
print "Recepteur à AHL=",(float(cpt14)/float(len(list_bacteria)))*100,"%","\n","\n"
 +
 +
 +
 +
 +
 +
 +
def color():
 +
r"""
 +
Color function to attribute a color for the bacteria according this state
 +
"""
 +
for j in range (0,len(list_bacteria)):
 +
#Bacteria with no state
 +
if list_bacteria[j][2]==0 or list_bacteria[j][2]==None or list_bacteria[j][3]==None or list_bacteria[j][4]==None: #white
 +
lxw.append(list_bacteria[j][0])
 +
lyw.append(list_bacteria[j][1])
 +
 +
#Bacteria with State 1
 +
if list_bacteria[j][5]==1 and list_bacteria[j][7]==1: #blue
 +
lxb.append(list_bacteria[j][0])
 +
lyb.append(list_bacteria[j][1])
 +
 +
#Bacteria with State 2
 +
if list_bacteria[j][8]==1 and list_bacteria[j][10]==1: #red
 +
lxr.append(list_bacteria[j][0])
 +
lyr.append(list_bacteria[j][1])
 +
 +
#Bacteria with State 3
 +
if list_bacteria[j][11]==1 and list_bacteria[j][13]==1: #green
 +
lxg.append(list_bacteria[j][0])
 +
lyg.append(list_bacteria[j][1])
 +
 +
#Bacteria with State 1 and State 2
 +
if list_bacteria[j][5]==1 and list_bacteria[j][7]==1 and list_bacteria[j][8]==1 and list_bacteria[j][10]==1: #black
 +
lxn.append(list_bacteria[j][0])
 +
lyn.append(list_bacteria[j][1])
 +
 +
def do_plot(name,titre):
 +
r"""
 +
Create a plot figure. Take 2 arguments : Name = name of picture and Title = title of plot
 +
"""
 +
color()
 +
plot(lxw,lyw,"wo",ms=5,linewidth=0)
 +
plot(lxr,lyr,"ro",ms=5,linewidth=0)
 +
plot(lxb,lyb,"bo",ms=5,linewidth=0)
 +
plot(lxg,lyg,"go",ms=5,linewidth=0)
 +
plot(lxn,lyn,"ko",ms=5,linewidth=0)
 +
axis((0,10,0,10))
 +
title(titre)
 +
savefig('fig'+name+'.png')
 +
 +
 +
 +
################################################################
 +
########################### MAIN ###############################
 +
################################################################
 +
for i in range (nb_bacteria):
for i in range (nb_bacteria):
List = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
List = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
Line 83: Line 525:
mutation()
mutation()
do_plot("4","tours2")
do_plot("4","tours2")
 +
stimulus_factor(0.15,rayon_action)
 +
mutation()
 +
do_plot("5","tours3")
 +
stimulus_factor(0.20,rayon_action)
 +
mutation()
 +
do_plot("6","tours4")
 +
statistic()
 +
stimulus_factor(0.25,rayon_action)
 +
mutation()
 +
do_plot("7","tours5")
 +
 +
os.system("python create_gif.py")
 +
 +
 +
 +
                                                 </pre>
                                                 </pre>
-
+
</p>
</div>
</div>
</div>
</div>

Revision as of 07:27, 24 September 2012

Modelling - iGEM Bordeaux 2012

  • Modelling

iGEM - Bordeaux - Source Code

Init_PEB.py file

r"""
File contains var
"""

__projet__ = 'iGEM '
__author__ = 'Djemiel Christophe, Freche Arnaud'
__copyright__ = 'Copyright (c) 2012 BordeauxTeam'
__license__ = ''
__vcs_id__ = '$Id$'
__version__ = '1.0'

#var 
directory_pictures="pictures_simulation/"

#initial parameters 
nb_bacteria=8000

#features constitutive
seuil_acivation_recepteur1=0.75
seuil_acivation_recepteur2=0.75
seuil_acivation_recepteur3=0.75

#mutation
seuil_mutation_operon=0.05
seuil_mutation_LasR=0.05
seuil_mutation_LuxS=0.05
seuil_mutation_BetaGal=0.05
seuil_mutation_LuxBox=0.05
seuil_mutation_LuxI=0.05
seuil_mutation_MCherry=0.05
seuil_mutation_QBox=0.05
seuil_mutation_LasI=0.05

#change state
seuil_etat1_2=0.05

#noise
noise_pourcent=0.0001
seuil_bruit1=0.33
seuil_bruit2=0.66

#stimulus light
seuil_transfo_lumiere=0.7
diameter_light=1

rayon_action=0.075

PEP.py file

#!/usr/bin/python
# -*- coding: iso-8859-1 -*-


import random
from pylab import *
from numpy import *
from init_PEB import *
import os 


list_bacteria = []
lxw=[]
lyw=[]
lxb=[]
lyb=[]
lxr=[]
lyr=[]
lxg=[]
lyg=[]
lxn=[]
lyn=[]


def features_bacteria ():
	r"""
	Function attribute all features at the bacteria
	"""
	#Coordinates
	x=random.uniform(0,10) # position x of the bacteria on the petri dish 
	List[0]=x
	y=random.uniform(0,10) # position x of the bacteria on the petri dish 
	List[1]=y
	
	#States
	state1=None 
	List[2]=state1
	state2=None 
	List[3]=state2
	state3=None 
	List[4]=state3
	
	#Operon 1
	LasR_box=None
	List[5]=LasR_box
	LuxS=None
	List[6]=LuxS
	Beta_gal=None
	List[7]=Beta_gal
	
	#Operon 2
	Lux_box=None
	List[8]=Lux_box
	LuxI=None
	List[9]=LuxI
	m_cherry=None
	List[10]=m_cherry
	
	#Operon 3
	Q_box=None
	List[11]=Q_box
	LasI=None
	List[12]=LasI
	GFP=None
	List[13]=GFP
	
	#Operon constitutive
	recepteur1=None
	List[14]=recepteur1
	recepteur2=None
	List[15]=recepteur2
	recepteur3=None
	List[16]=recepteur3

	return List


	
def feature_constitutive():

	for j in range (0,len(list_bacteria)):
		proba_active_14=random.uniform(0,1)
		proba_active_15=random.uniform(0,1)
		proba_active_16=random.uniform(0,1)
		
		if proba_active_14<=seuil_acivation_recepteur1:
			list_bacteria[j][14]=1
		else:
			list_bacteria[j][14]=0
			
		if proba_active_15<=seuil_acivation_recepteur2:
			list_bacteria[j][15]=1
		else:
			list_bacteria[j][15]=0
			
		if proba_active_16<=seuil_acivation_recepteur3:
			list_bacteria[j][16]=1
		else:
			list_bacteria[j][16]=0

def mutation():

	for j in range (0,len(list_bacteria)):
		proba_mutation=random.uniform(0.1)
		if proba_mutation<=0.05:
			proba_mutation_LasR=random.uniform(0.1)
			proba_mutation_LuxS=random.uniform(0.1)
			proba_mutation_BetaGal=random.uniform(0.1)
			proba_mutation_LuxBox=random.uniform(0.1)
			proba_mutation_LuxI=random.uniform(0.1)
			proba_mutation_MCherry=random.uniform(0.1)
			proba_mutation_QBox=random.uniform(0.1)
			proba_mutation_LasI=random.uniform(0.1)
			proba_mutation_GFP=random.uniform(0.1)
			if proba_mutation_LasR<=seuil_mutation_LasR:
				list_bacteria[j][5]=0
			if proba_mutation_LuxS<=seuil_mutation_LuxS:
				list_bacteria[j][6]=0
			if proba_mutation_BetaGal<=seuil_mutation_BetaGal:
				list_bacteria[j][7]=0
			if proba_mutation_LuxBox<=seuil_mutation_LuxBox:
				list_bacteria[j][8]=0
			if proba_mutation_LuxI<=seuil_mutation_LuxI:
				list_bacteria[j][9]=0
			if proba_mutation_MCherry<=seuil_mutation_MCherry:
				list_bacteria[j][10]=0
			if proba_mutation_QBox<=seuil_mutation_QBox:
				list_bacteria[j][11]=0
			if proba_mutation_LasI<=seuil_mutation_LasI:
				list_bacteria[j][12]=0
			if proba_mutation_GFP<=seuil_mutation_GFP:
				list_bacteria[j][13]=0
			

def active_state():
	r"""
	Function permit to active the state of the bacteria according the activation of these genes
	"""
	for j in range (0,len(list_bacteria)):
		#State 1
		if list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][7]==1:
				list_bacteria[j][2]=1
				list_bacteria[j][3]=0
				list_bacteria[j][4]=0
		
		#State 2
		if list_bacteria[j][8]==1 and list_bacteria[j][9]==1 and list_bacteria[j][10]==1:
				list_bacteria[j][2]=0
				list_bacteria[j][3]=1
				list_bacteria[j][4]=0
		
		#State 3	
		if list_bacteria[j][11]==1 and list_bacteria[j][12]==1 and list_bacteria[j][13]==1:
				list_bacteria[j][2]=0
				list_bacteria[j][3]=0
				list_bacteria[j][4]=1

def change_state():
	r"""
	Function permit to the bacteria changing state
	"""
	for j in range (0,len(list_bacteria)):
		# State 1 --> State 2
		if  list_bacteria[j][2]==1 and list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][14]==1:
			proba=random.uniform(0,1)
			if proba<=seuil_etat1_2:
				list_bacteria[j][8] =1
				list_bacteria[j][9] =1
				list_bacteria[j][10] =1
				
def noise(noise_pourcent):
	r"""
	Create a noise before the first stimulation light. Take one argument : noise_pourcent = the noise that we want
	"""
	for j in range (0,len(list_bacteria)):
		proba=random.uniform(0,1)
		if proba<=noise_pourcent:
			proba2=random.uniform(0,1)
			if 0<=proba2

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