Team:Bordeaux/SourceCodeModelling

From 2012.igem.org

(Difference between revisions)
Line 292: Line 292:
list_bacteria[j][9] =1
list_bacteria[j][9] =1
list_bacteria[j][10] =1
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 :
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        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():
def stimulus_light():
r"""
r"""

Revision as of 08:11, 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 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")

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