Team:USTC Software/WhatCooperation

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(New page: [https://static.igem.org/mediawiki/2009/thumb/7/79/S-m-2-1.jpg/500px-S-m-2-1.jpg ] == '''pConX<sub>2</sub>+LuxR+pLux/Tet+GFP''' == '''Parts:''' <partinfo>K176026</partinfo> <partinfo>K176...)
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==Introduction==
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We help [https://2009.igem.org/Team:USTC_Software USTC Wet Team] ''identify the kinetic parameters'' in '''pConX<sub>2</sub>+LuxR+pLux/Tet+GFP''' device.
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The completion of this [https://2009.igem.org/Team:USTC/Modeling/Model-2 model] are a result of collaboration. With the permission from both teams, we share the source code of this description page together
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==pConX<sub>2</sub>+LuxR+pLux/Tet+GFP==
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== '''pConX<sub>2</sub>+LuxR+pLux/Tet+GFP''' ==
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'''Parts:'''   
'''Parts:'''   
<partinfo>K176026</partinfo> <partinfo>K176026 DeepComponents</partinfo>
<partinfo>K176026</partinfo> <partinfo>K176026 DeepComponents</partinfo>
<partinfo>K176126</partinfo> <partinfo>K176128</partinfo> <partinfo>K176130</partinfo>  
<partinfo>K176126</partinfo> <partinfo>K176128</partinfo> <partinfo>K176130</partinfo>  
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==Reactions and ODE==
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== '''Simplified Model-2''' ==
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==A Simplified Model==
We employed an ODE model. We defined the input to be AHL<sub>out</sub> the and the output to be the synthesis rate of mature GFP. In this system,we assumed the concentration of the LuxR was constant.
We employed an ODE model. We defined the input to be AHL<sub>out</sub> the and the output to be the synthesis rate of mature GFP. In this system,we assumed the concentration of the LuxR was constant.
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From above equations, we can the change of PoPS respond to the AHL<sub>in</sub>.
From above equations, we can the change of PoPS respond to the AHL<sub>in</sub>.
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For this system, the value of parameter d, 0.00847, could be estimated based on the measurement of the OD. For instance, when the concentration of AHL<sub>out</sub> was zero, the value of d was 0.00368 per minute. The values of 4.8E-3 per sec for rmG, 1.8E-3 per sec for a and 0.4 per sec for pG were got from the experiment conducted by Barry Canton and Anna Labno in 2004, click [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis here] to the details.
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For this system, the value of parameter d, 0.00847, could be estimated based on the measurement of the OD. For instance, when the concentration of AHL<sub>out</sub> was zero, the value of d was 0.00368 per minute. The values of 4.8E-3 per sec for rmG, 1.8E-3 per sec for a and 0.4 per sec for pG were got from the experiment conducted by Barry Canton and Anna Labno in 2004, click [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis here] to the details.
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With the help of [https://2009.igem.org/Team:USTC_Software USTC_Software], we succeeded to estimate the values of k<sub>3</sub>, r<sub>AHLin</sub>, C<sub>1</sub>, C<sub>2</sub>, C<sub>3</sub> and C<sub>4</sub>. The simulation results as follows.
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==Identification Results==
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k3=0.8; rAHL=0.001;
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With the help of [https://2009.igem.org/Team:USTC USTC Wet Team], we succeeded to estimate the values of k<sub>3</sub>, r<sub>AHLin</sub>, C<sub>1</sub>, C<sub>2</sub>, C<sub>3</sub> and C<sub>4</sub>. The simulation results as follows.
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C1=1.5*10^(-10); C2=1*10^(10); C3=8*10^(-7); C4=5.8*10^(11)
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===Parameters===
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'''k3=0.8; rAHL=0.001; C1=1.5*10^(-10); C2=1*10^(10); C3=8*10^(-7); C4=5.8*10^(11)'''
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===Identification Results Comparison With Raw Data===
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In this picture, the dots were the measuring poingts in our system and the curves were the corresponding simulations to a particular concentration of AHL<sub>out</sub>.
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In this picture, the dots were the measuring poingts in our system and the curves were the corresponding simulations to a particular concentration of AHL<sub>out</sub>.
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In picture below, the dots were the measuring poingts in our system and the surface was the corresponding simulation.
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Latest revision as of 03:45, 22 October 2009


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Contents

Introduction

We help USTC Wet Team identify the kinetic parameters in pConX2+LuxR+pLux/Tet+GFP device. The completion of this model are a result of collaboration. With the permission from both teams, we share the source code of this description page together

pConX2+LuxR+pLux/Tet+GFP

Parts:


Reactions and ODE

A Simplified Model

We employed an ODE model. We defined the input to be AHLout the and the output to be the synthesis rate of mature GFP. In this system,we assumed the concentration of the LuxR was constant.

To simplify the model, the (Recation S2-4), (Recation S2-5) and (Recation S2-6) were considered to be able to get balance in a very short time.

From above equations, we can the change of PoPS respond to the AHLin.

For this system, the value of parameter d, 0.00847, could be estimated based on the measurement of the OD. For instance, when the concentration of AHLout was zero, the value of d was 0.00368 per minute. The values of 4.8E-3 per sec for rmG, 1.8E-3 per sec for a and 0.4 per sec for pG were got from the experiment conducted by Barry Canton and Anna Labno in 2004, click here to the details.

Identification Results

With the help of USTC Wet Team, we succeeded to estimate the values of k3, rAHLin, C1, C2, C3 and C4. The simulation results as follows.

Parameters

k3=0.8; rAHL=0.001; C1=1.5*10^(-10); C2=1*10^(10); C3=8*10^(-7); C4=5.8*10^(11)

Identification Results Comparison With Raw Data

In this picture, the dots were the measuring poingts in our system and the curves were the corresponding simulations to a particular concentration of AHLout.

In picture below, the dots were the measuring poingts in our system and the surface was the corresponding simulation.

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