Team:Bordeaux/SourceCodeModelling

From 2012.igem.org

(Difference between revisions)
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<hr>
</br>
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<pre class="prettyprint lang-py">
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<a href="http://cdjemiel.free.fr/igem2012/code/PEB.py" title="Mst" target="_blank">Download file PEP.py</a>
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#!/usr/bin/python
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# -*- coding: iso-8859-1 -*-
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import random
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from pylab import *
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from numpy import *
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from init_PEB import *
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import os
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list_bacteria = []
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lxw=[]
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lyw=[]
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lxb=[]
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lyb=[]
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lxr=[]
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lyr=[]
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lxg=[]
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lyg=[]
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lxn=[]
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lyn=[]
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def features_bacteria ():
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r'''
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Function attribute all features at the bacteria
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'''
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#Coordinates
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x=random.uniform(0,10) # position x of the bacteria on the petri dish
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List[0]=x
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y=random.uniform(0,10) # position x of the bacteria on the petri dish
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List[1]=y
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#States
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state1=None
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List[2]=state1
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state2=None
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List[3]=state2
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state3=None
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List[4]=state3
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#Operon 1
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LasR_box=None
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List[5]=LasR_box
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LuxS=None
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List[6]=LuxS
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Beta_gal=None
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List[7]=Beta_gal
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#Operon 2
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Lux_box=None
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List[8]=Lux_box
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LuxI=None
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List[9]=LuxI
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m_cherry=None
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List[10]=m_cherry
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#Operon 3
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Q_box=None
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List[11]=Q_box
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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
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def feature_constitutive():
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for j in range (0,len(list_bacteria)):
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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
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else:
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list_bacteria[j][14]=0
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if proba_active_15<=seuil_acivation_recepteur2:
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list_bacteria[j][15]=1
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else:
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list_bacteria[j][15]=0
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if proba_active_16<=seuil_acivation_recepteur3:
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list_bacteria[j][16]=1
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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:
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proba_mutation_LasR=random.uniform(0.1)
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proba_mutation_LuxS=random.uniform(0.1)
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proba_mutation_BetaGal=random.uniform(0.1)
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proba_mutation_LuxBox=random.uniform(0.1)
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proba_mutation_LuxI=random.uniform(0.1)
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proba_mutation_MCherry=random.uniform(0.1)
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proba_mutation_QBox=random.uniform(0.1)
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proba_mutation_LasI=random.uniform(0.1)
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proba_mutation_GFP=random.uniform(0.1)
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if proba_mutation_LasR<=seuil_mutation_LasR:
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list_bacteria[j][5]=0
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if proba_mutation_LuxS<=seuil_mutation_LuxS:
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list_bacteria[j][6]=0
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if proba_mutation_BetaGal<=seuil_mutation_BetaGal:
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list_bacteria[j][7]=0
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if proba_mutation_LuxBox<=seuil_mutation_LuxBox:
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list_bacteria[j][8]=0
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if proba_mutation_LuxI<=seuil_mutation_LuxI:
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list_bacteria[j][9]=0
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if proba_mutation_MCherry<=seuil_mutation_MCherry:
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list_bacteria[j][10]=0
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if proba_mutation_QBox<=seuil_mutation_QBox:
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list_bacteria[j][11]=0
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if proba_mutation_LasI<=seuil_mutation_LasI:
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list_bacteria[j][12]=0
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if proba_mutation_GFP<=seuil_mutation_GFP:
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list_bacteria[j][13]=0
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def active_state():
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r'''
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Function permit to active the state of the bacteria according the activation of these genes
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'''
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for j in range (0,len(list_bacteria)):
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#State 1
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if list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][7]==1:
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list_bacteria[j][2]=1
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list_bacteria[j][3]=0
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list_bacteria[j][4]=0
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#State 2
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if list_bacteria[j][8]==1 and list_bacteria[j][9]==1 and list_bacteria[j][10]==1:
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list_bacteria[j][2]=0
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list_bacteria[j][3]=1
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list_bacteria[j][4]=0
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#State 3
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if list_bacteria[j][11]==1 and list_bacteria[j][12]==1 and list_bacteria[j][13]==1:
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list_bacteria[j][2]=0
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list_bacteria[j][3]=0
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list_bacteria[j][4]=1
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def change_state():
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r'''
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Function permit to the bacteria changing state
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'''
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for j in range (0,len(list_bacteria)):
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# State 1 --> State 2
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if  list_bacteria[j][2]==1 and list_bacteria[j][5]==1 and list_bacteria[j][6]==1 and list_bacteria[j][14]==1:
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proba=random.uniform(0,1)
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if proba<=seuil_etat1_2:
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list_bacteria[j][8] =1
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list_bacteria[j][9] =1
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list_bacteria[j][10] =1
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def noise(noise_pourcent):
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r'''
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Create a noise before the first stimulation light. Take one argument : noise_pourcent = the noise that we want
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'''
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for j in range (0,len(list_bacteria)):
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proba=random.uniform(0,1)
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if proba<=noise_pourcent:
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proba2=random.uniform(0,1)
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if 0<=proba2<seuil_bruit1:
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list_bacteria[j][5]=1
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list_bacteria[j][6]=1
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list_bacteria[j][7]=1
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if seuil_bruit1<=proba2<seuil_bruit2:
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list_bacteria[j][8]=1
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list_bacteria[j][9]=1
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list_bacteria[j][10]=1
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if seuil_bruit2<=proba2<1:
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list_bacteria[j][11]=1
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list_bacteria[j][12]=1
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list_bacteria[j][13]=1
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def stimulus_light():
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r'''
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Function create the first stimulation light
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'''
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for j in range (0,len(list_bacteria)):
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proba_recepteur=random.uniform(0,1)
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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:
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proba=random.uniform(0,1)
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if proba<=seuil_transfo_lumiere:
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list_bacteria[j][5]=1
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list_bacteria[j][6]=1
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list_bacteria[j][7]=1
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def stimulus_factor(x,rayon_action):
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r'''
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Function create others stimulations
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'''
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change_state()
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active_state()
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for j in range (0,len(list_bacteria)):
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#stimulus facteur1
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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:
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for i in range (0,len(list_bacteria)):
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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 :
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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]))
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proba=random.uniform(0,1)
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if proba*distance_voisin<=x:
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list_bacteria[j][8] =1
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list_bacteria[j][9] =1
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list_bacteria[j][10] =1
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change_state()
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active_state()
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for j in range (0,len(list_bacteria)):
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#stimulus facteur2
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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:
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for i in range (0,len(list_bacteria)):
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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 :
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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]))
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proba=random.uniform(0,1)
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if proba*distance_voisin<=x:
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list_bacteria[j][11] =1
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list_bacteria[j][12] =1
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list_bacteria[j][13] =1
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change_state()
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active_state()
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for j in range (0,len(list_bacteria)):
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#stimulus facteur2
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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:
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for i in range (0,len(list_bacteria)):
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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 :
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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]))
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proba=random.uniform(0,1)
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if proba*distance_voisin<=x:
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list_bacteria[j][5] =1
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list_bacteria[j][6] =1
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list_bacteria[j][7] =1
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change_state()
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active_state()
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def statistic():
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cpt1=0
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cpt2=0
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cpt3=0
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cpt4=0
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cpt5=0
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cpt6=0
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cpt7=0
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cpt8=0
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cpt9=0
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cpt10=0
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cpt11=0
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cpt12=0
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cpt13=0
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cpt14=0
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cpt15=0
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cpt16=0
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for j in range (0,len(list_bacteria)):
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if list_bacteria[j][2]==1:
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cpt1=cpt1+1
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if list_bacteria[j][3]==1:
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cpt2=cpt2+1
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if list_bacteria[j][4]==1:
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cpt3=cpt3+1
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if list_bacteria[j][5]==1:
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cpt4=cpt4+1
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if list_bacteria[j][6]==1:
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cpt5=cpt5+1
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if list_bacteria[j][7]==1 and list_bacteria[j][2]==1:
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cpt6=cpt6+1
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if list_bacteria[j][8]==1:
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cpt7=cpt7+1
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if list_bacteria[j][9]==1:
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cpt8=cpt8+1
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if list_bacteria[j][10]==1 and list_bacteria[j][3]==1:
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cpt9=cpt9+1
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if list_bacteria[j][11]==1:
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cpt10=cpt10+1
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if list_bacteria[j][12]==1:
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cpt11=cpt11+1
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if list_bacteria[j][13]==1 and list_bacteria[j][4]==1:
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cpt12=cpt12+1
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if list_bacteria[j][14]==1:
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cpt13=cpt13+1
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if list_bacteria[j][15]==1:
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cpt14=cpt14+1
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if list_bacteria[j][16]==1:
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cpt15=cpt15+1
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if list_bacteria[j][5]==1 and list_bacteria[j][7]==1 and list_bacteria[j][8]==1 and list_bacteria[j][10]==1:
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cpt16=cpt16+1
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print "\n","\n"
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print "OPERON A:"
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print "etat1=",(float(cpt1)/float(len(list_bacteria)))*100,"%"
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print "etat1 et etat2 à la fois=",(float(cpt16)/float(len(list_bacteria)))*100,"%"
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print "Las R actif=",(float(cpt4)/float(len(list_bacteria)))*100,"%"
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print "Production de Borat =",(float(cpt5)/float(len(list_bacteria)))*100,"%"
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print "Production BetaGal=",(float(cpt6)/float(len(list_bacteria)))*100,"%"
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print "Recepteur à PAI-1 actif=",(float(cpt15)/float(len(list_bacteria)))*100,"%","\n","\n"
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-
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print "OPERON B:"
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print "etat2=",(float(cpt2)/float(len(list_bacteria)))*100,"%"
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print "Lux Box fonctionnelle=",(float(cpt7)/float(len(list_bacteria)))*100,"%"
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print "Production de AHL=",(float(cpt8)/float(len(list_bacteria)))*100,"%"
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-
print "Production de M-Cherry=",(float(cpt9)/float(len(list_bacteria)))*100,"%"
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print "Recepteur à Borat actif=",(float(cpt13)/float(len(list_bacteria)))*100,"%","\n","\n"
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print "OPERON C:"
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print "etat3=",(float(cpt3)/float(len(list_bacteria)))*100,"%"
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print "Q Box fonctionnelle=",(float(cpt10)/float(len(list_bacteria)))*100,"%"
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print "Production de PAI-1=",(float(cpt11)/float(len(list_bacteria)))*100,"%"
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print "Production de GFP=",(float(cpt12)/float(len(list_bacteria)))*100,"%"
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print "Recepteur à AHL=",(float(cpt14)/float(len(list_bacteria)))*100,"%","\n","\n"
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def color():
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r'''
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Color function to attribute a color for the bacteria according this state
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'''
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for j in range (0,len(list_bacteria)):
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#Bacteria with no state
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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
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lxw.append(list_bacteria[j][0])
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lyw.append(list_bacteria[j][1])
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-
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#Bacteria with State 1
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if list_bacteria[j][5]==1 and list_bacteria[j][7]==1: #blue
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lxb.append(list_bacteria[j][0])
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lyb.append(list_bacteria[j][1])
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-
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#Bacteria with State 2
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if list_bacteria[j][8]==1 and list_bacteria[j][10]==1: #red
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lxr.append(list_bacteria[j][0])
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lyr.append(list_bacteria[j][1])
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-
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#Bacteria with State 3
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if list_bacteria[j][11]==1 and list_bacteria[j][13]==1: #green
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lxg.append(list_bacteria[j][0])
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lyg.append(list_bacteria[j][1])
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-
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#Bacteria with State 1 and State 2
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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
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lxn.append(list_bacteria[j][0])
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lyn.append(list_bacteria[j][1])
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-
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def do_plot(name,titre):
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r'''
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Create a plot figure. Take 2 arguments : Name = name of picture and Title = title of plot
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-
'''
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color()
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plot(lxw,lyw,"wo",ms=5,linewidth=0)
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-
plot(lxr,lyr,"ro",ms=5,linewidth=0)
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plot(lxb,lyb,"bo",ms=5,linewidth=0)
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plot(lxg,lyg,"go",ms=5,linewidth=0)
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plot(lxn,lyn,"ko",ms=5,linewidth=0)
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axis((0,10,0,10))
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title(titre)
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savefig('fig'+name+'.png')
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-
 
+
-
 
+
-
 
+
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################################################################
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-
########################### MAIN ###############################
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-
################################################################
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-
 
+
-
for i in range (nb_bacteria):
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List = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
+
-
features_bacteria()
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list_bacteria.append(List)
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-
 
+
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feature_constitutive()
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-
do_plot("0","temps0")
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mutation()
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-
noise(noise_pourcent)
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-
active_state()
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-
do_plot("1","bruit")
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stimulus_light()
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active_state()
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do_plot("2","light")
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stimulus_factor(0.05,rayon_action)
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mutation()
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do_plot("3","tours1")
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stimulus_factor(0.10,rayon_action)
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mutation()
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-
do_plot("4","tours2")
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stimulus_factor(0.15,rayon_action)
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mutation()
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do_plot("5","tours3")
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stimulus_factor(0.20,rayon_action)
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-
mutation()
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do_plot("6","tours4")
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statistic()
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-
stimulus_factor(0.25,rayon_action)
+
-
mutation()
+
-
do_plot("7","tours5")
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-
 
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#os.system("python create_gif.py")
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                                                </pre>
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</p>
</p>
</div>
</div>

Revision as of 08:41, 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


Download file PEP.py

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