Team:Bordeaux/SourceCodeModelling

From 2012.igem.org

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Line 64: Line 64:
<h4>Init_PEB.py file</h4>
<h4>Init_PEB.py file</h4>
<hr>
<hr>
 +
</br>
 +
<li><a href="http://cdjemiel.free.fr/igem2012/code/init_PEB.py" title="Mst" target="_blank">Download file PEP.py</a></li>
</br>
</br>
Line 99: Line 101:
seuil_mutation_QBox=0.05
seuil_mutation_QBox=0.05
seuil_mutation_LasI=0.05
seuil_mutation_LasI=0.05
 +
seuil_mutation_GFP=0.05
#change state
#change state
Line 119: Line 122:
<p>
<p>
-
<h4>PEP.py file</h4>
+
<h4>PEB.py file (Main program)</h4>
<hr>
<hr>
</br>
</br>
 +
<li><a href="http://cdjemiel.free.fr/igem2012/code/PEB.py" title="Mst" target="_blank">Download file PEB.py</a></li>
 +
</p>
-
                                                <pre class="prettyprint lang-py">
+
<p>
-
#!/usr/bin/python
+
<h4>Create a gif </h4>
-
# -*- coding: iso-8859-1 -*-
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<hr>
-
 
+
</br>
-
 
+
<li><a href="http://cdjemiel.free.fr/igem2012/code/create_gif.py" title="Mst" target="_blank">Download file create_gif.py</a></li>
-
import random
+
<li><a href="http://cdjemiel.free.fr/igem2012/code/images2gif.py" title="Mst" target="_blank">Download file images2gif.py</a></li>
-
from pylab import *
+
</br>
-
from numpy import *
+
Reference : <a href="http://www.somethinkodd.com/oddthinking/2005/12/06/python-imaging-library-pil-and-animated-gifs/" target="_blank">Python Imaging Library (PIL) and Animated GIFs</a>
-
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
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-
List[2]=state1
+
-
state2=None
+
-
List[3]=state2
+
-
state3=None
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-
List[4]=state3
+
-
+
-
#Operon 1
+
-
LasR_box=None
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-
List[5]=LasR_box
+
-
LuxS=None
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-
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
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List[12]=LasI
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-
GFP=None
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List[13]=GFP
+
-
+
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#Operon constitutive
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-
recepteur1=None
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-
List[14]=recepteur1
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-
recepteur2=None
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-
List[15]=recepteur2
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-
recepteur3=None
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-
List[16]=recepteur3
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-
 
+
-
return List
+
-
 
+
-
 
+
-
+
-
def feature_constitutive():
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-
 
+
-
for j in range (0,len(list_bacteria)):
+
-
proba_active_14=random.uniform(0,1)
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-
proba_active_15=random.uniform(0,1)
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-
proba_active_16=random.uniform(0,1)
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-
+
-
if proba_active_14<=seuil_acivation_recepteur1:
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list_bacteria[j][14]=1
+
-
else:
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list_bacteria[j][14]=0
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-
+
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if proba_active_15<=seuil_acivation_recepteur2:
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list_bacteria[j][15]=1
+
-
else:
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-
list_bacteria[j][15]=0
+
-
+
-
if proba_active_16<=seuil_acivation_recepteur3:
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list_bacteria[j][16]=1
+
-
else:
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-
list_bacteria[j][16]=0
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-
 
+
-
def mutation():
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-
 
+
-
for j in range (0,len(list_bacteria)):
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-
proba_mutation=random.uniform(0.1)
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-
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):
+
-
List = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
+
-
features_bacteria()
+
-
list_bacteria.append(List)
+
-
 
+
-
feature_constitutive()
+
-
do_plot("0","temps0")
+
-
mutation()
+
-
noise(noise_pourcent)
+
-
active_state()
+
-
do_plot("1","bruit")
+
-
stimulus_light()
+
-
active_state()
+
-
do_plot("2","light")
+
-
stimulus_factor(0.05,rayon_action)
+
-
mutation()
+
-
do_plot("3","tours1")
+
-
stimulus_factor(0.10,rayon_action)
+
-
mutation()
+
-
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>
+
</p>
</p>
</div>
</div>

Latest revision as of 09:29, 26 September 2012

Modelling - iGEM Bordeaux 2012

  • Modelling

iGEM - Bordeaux - Source Code

Init_PEB.py file


  • Download file PEP.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
seuil_mutation_GFP=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

    PEB.py file (Main program)


  • Download file PEB.py

    • Create a gif


  • Download file create_gif.py
  • Download file images2gif.py

    • Reference : Python Imaging Library (PIL) and Animated GIFs

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    Retrieved from "http://2012.igem.org/Team:Bordeaux/SourceCodeModelling"