Team:Bordeaux/RealisationModelling
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All these characteristics are stocked into a list <b>List</b>. | All these characteristics are stocked into a list <b>List</b>. | ||
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Indeed this permit us to test some variations on the different activity of the operons responsibles of cellular communication. | Indeed this permit us to test some variations on the different activity of the operons responsibles of cellular communication. | ||
Parameters can be modified in the files init_PEB.py. | Parameters can be modified in the files init_PEB.py. | ||
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Indeed if a gene that synthesize a protein that activate another operon is mutated his value will be 0. | Indeed if a gene that synthesize a protein that activate another operon is mutated his value will be 0. | ||
All these parameters can be modified and chose by the user ine the file init_PEB.py. | All these parameters can be modified and chose by the user ine the file init_PEB.py. | ||
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We put a function <b>active_state()</b> to activate the state and phenotype of the bacteria. This function modify the value none to 1. | We put a function <b>active_state()</b> to activate the state and phenotype of the bacteria. This function modify the value none to 1. | ||
That activation depends on activated genes. | That activation depends on activated genes. | ||
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We also made a function <b>change_state()</b> to make special modification of the state 1 to state 2, this is due to a little possible leak of our construction. | We also made a function <b>change_state()</b> to make special modification of the state 1 to state 2, this is due to a little possible leak of our construction. | ||
It is the only modification from an activated state to another possible and permited in the simulation. | It is the only modification from an activated state to another possible and permited in the simulation. | ||
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In real bacteria culture this phenomenon is often present, and this function try to mimic this problem . | In real bacteria culture this phenomenon is often present, and this function try to mimic this problem . | ||
This function was really necessary because this phenomenon can have big influence on the results (see the result pat). | This function was really necessary because this phenomenon can have big influence on the results (see the result pat). | ||
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The function <b>stimulus_light()</b> permit to simulate the beginning point of the simulation. The induction is realized at the center of the grid as a circle. | The function <b>stimulus_light()</b> permit to simulate the beginning point of the simulation. The induction is realized at the center of the grid as a circle. | ||
All the bacteria in this area are going to have their gene 1 activated(none ->1). | All the bacteria in this area are going to have their gene 1 activated(none ->1). | ||
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Revision as of 14:47, 23 September 2012
iGEM - Bordeaux - Realisation
To carry out that modeling and simulation software, we chose python programming language. This choice has be taken due to short time available and few number of programmers for this project. Python is a high level programming language, interpreted, it permits to create simple and easy programs with a clear syntax and have lots of libraries available.
Functions
We are now showing all of the function create for this modeling. The function features_bacteria () permits to give all the characteristics to each 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] 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")