Team:Bordeaux/SourceCodeModelling

From 2012.igem.org

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<h4>Init_PEB.py file</h4>
<h4>Init_PEB.py file</h4>
<hr>
<hr>
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</br>
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<li><a href="http://cdjemiel.free.fr/igem2012/code/init_PEB.py" title="Mst" target="_blank">Download file PEP.py</a></li>
</br>
</br>
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seuil_mutation_QBox=0.05
seuil_mutation_QBox=0.05
seuil_mutation_LasI=0.05
seuil_mutation_LasI=0.05
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seuil_mutation_GFP=0.05
#change state
#change state
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rayon_action=0.075
rayon_action=0.075
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                                                </pre>
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</pre>
</p>
</p>
<p>
<p>
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<h4>PEP.py file</h4>
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<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>
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</p>
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                                                <pre class="prettyprint lang-py">
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<p>
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#!/usr/bin/python
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<h4>Create a gif </h4>
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# -*- coding: iso-8859-1 -*-
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<hr>
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</br>
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<li><a href="http://cdjemiel.free.fr/igem2012/code/create_gif.py" title="Mst" target="_blank">Download file create_gif.py</a></li>
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import random
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<li><a href="http://cdjemiel.free.fr/igem2012/code/images2gif.py" title="Mst" target="_blank">Download file images2gif.py</a></li>
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from pylab import *
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</br>
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from numpy import *
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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>
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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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                                                </pre>
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</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"