Team:Groningen/Modelling/Characterization

From 2009.igem.org

(Difference between revisions)
m
(Ignoring most experiments and focussing on just a few variables.)
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<script type="text/javascript" src="/Team:Groningen/Modelling/Model.js?action=raw"></script>
<script type="text/javascript" src="/Team:Groningen/Modelling/Model.js?action=raw"></script>
<script type="text/javascript">
<script type="text/javascript">
-
var experiments = {Meng2004:
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var experiments = {/*Meng2004:
                   {constants:{Vc:0.0073,Vs:(1.1-0.0073),beta4:0,pro:0,ars2T:0},AsT:10e-6,
                   {constants:{Vc:0.0073,Vs:(1.1-0.0073),beta4:0,pro:0,ars2T:0},AsT:10e-6,
                     data:{AsinT:[101.917808219178e-6,394.520547945205e-6,723.287671232877e-6,
                     data:{AsinT:[101.917808219178e-6,394.520547945205e-6,723.287671232877e-6,
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                   {constants:{Vc:0.000808081,Vs:(1-0.000808081),pro:0,ars2T:0},time:Infinity,
                   {constants:{Vc:0.000808081,Vs:(1-0.000808081),pro:0,ars2T:0},time:Infinity,
                     data:{AsinT:[207.0208222e-6,229.0443139e-6,493.3262146e-6,585.8248799e-6],
                     data:{AsinT:[207.0208222e-6,229.0443139e-6,493.3262146e-6,585.8248799e-6],
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                           AsT:[10e-6,20e-6,50e-6,100e-6]}},
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                           AsT:[10e-6,20e-6,50e-6,100e-6]}},*/
                   pSB1A2time:  //  concentration mode this is our first icps measerment wild type
                   pSB1A2time:  //  concentration mode this is our first icps measerment wild type
                   {constants:{Vc:0.002320346,Vs:(1-0.002320346),pro:0,ars2T:0},AsT:10e-6,
                   {constants:{Vc:0.002320346,Vs:(1-0.002320346),pro:0,ars2T:0},AsT:10e-6,
                     data:{AsinT:[66.07047517e-6,83.68926855e-6,114.522157e-6,132.1409503e-6,207.0208222e-6],
                     data:{AsinT:[66.07047517e-6,83.68926855e-6,114.522157e-6,132.1409503e-6,207.0208222e-6],
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                           time:[180,600,1200,2400,3600]}},
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                           time:[180,600,1200,2400,3600]}}/*,
                   pArsRRFPcon: // here the cell only contains extra RFP behind the the extra ArsR promotors.
                   pArsRRFPcon: // here the cell only contains extra RFP behind the the extra ArsR promotors.
                                 //    We incorporate this in our model by pretending RFP=GVP (1st icps)
                                 //    We incorporate this in our model by pretending RFP=GVP (1st icps)
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                   {constants:{Vc:0.003333333,Vs:(1-0.003333333),pro:0},AsT:10e-6,
                   {constants:{Vc:0.003333333,Vs:(1-0.003333333),pro:0},AsT:10e-6,
                     data:{AsinT:[52.85638014e-6,92.49866524e-6,88.0939669e-6,136.5456487e-6],
                     data:{AsinT:[52.85638014e-6,92.49866524e-6,88.0939669e-6,136.5456487e-6],
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                           time:[180,600,2400,3600]}}};   
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                           time:[180,600,2400,3600]}}*/};   
/*var varsToMutate = ['K5','v5','K7','k8','tauB','beta4','tauR','beta1','tauF','betaF',
/*var varsToMutate = ['K5','v5','K7','k8','tauB','beta4','tauR','beta1','tauF','betaF',
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                   beta5: function(v){return v.beta5;}};*/
                   beta5: function(v){return v.beta5;}};*/
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var varsToMutate = ['v5_K5','v5','k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4'/*,'tauFbetaF','betaF',
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var varsToMutate = [/*'v5_K5','v5',*/'k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4'/*,'tauFbetaF','betaF',
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                     'tauKbetaK','betaK','tauGbeta5','beta5'*/,'tauF','betaF','tauK','betaK','tauG','beta5','ars2T'];
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                     'tauKbetaK','betaK','tauGbeta5','beta5','tauF','betaF','tauK','betaK','tauG','beta5','ars2T'*/];
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var mutateFuncs = {v5: function(v){return v.v5;},
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var mutateFuncs = {//v5: function(v){return v.v5;},
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                   K5: function(v){return v.v5/v.v5_K5;},
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                   //K5: function(v){return v.v5/v.v5_K5;},
                   k8: function(v){return v.k8;},
                   k8: function(v){return v.k8;},
                   K7: function(v){return v.k8/v.k8_K7;},
                   K7: function(v){return v.k8/v.k8_K7;},
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                   tauR: function(v){return v.tauR_tauB*v.tauBbeta4/v.beta4;},
                   tauR: function(v){return v.tauR_tauB*v.tauBbeta4/v.beta4;},
                   beta4: function(v){return v.beta4;},
                   beta4: function(v){return v.beta4;},
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                   tauF: function(v){return v.tauF;},
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                   //tauF: function(v){return v.tauF;},
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                   betaF: function(v){return v.betaF;},
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                   //betaF: function(v){return v.betaF;},
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                   tauK: function(v){return v.tauK;},
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                   //tauK: function(v){return v.tauK;},
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                   betaK: function(v){return v.betaK;},
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                   //betaK: function(v){return v.betaK;},
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                   tauG: function(v){return v.tauG;},
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                   //tauG: function(v){return v.tauG;},
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                   ars2T: function(v){return v.ars2T;},
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                   //ars2T: function(v){return v.ars2T;},
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                   beta5: function(v){return v.beta5;},
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                   //beta5: function(v){return v.beta5;},
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                   beta1: function(v){return v.beta4*v.beta1_beta4;/*},
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                   beta1: function(v){return v.beta4*v.beta1_beta4;}/*,
                   tauF: function(v){return v.tauFbetaF/v.betaF;},
                   tauF: function(v){return v.tauFbetaF/v.betaF;},
                   betaF: function(v){return v.betaF;},
                   betaF: function(v){return v.betaF;},
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                   betaK: function(v){return v.betaK;},
                   betaK: function(v){return v.betaK;},
                   tauG: function(v){return v.tauGbeta5/v.beta5;},
                   tauG: function(v){return v.tauGbeta5/v.beta5;},
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                   beta5: function(v){return v.beta5;*/}};
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                   beta5: function(v){return v.beta5;}*/};
function computeCost(v,e) {
function computeCost(v,e) {
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function fitConstants() {
function fitConstants() {
   // Construct plots
   // Construct plots
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   constructPlot('v5K5plot');
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   //constructPlot('v5K5plot');
   constructPlot('k8K7plot');
   constructPlot('k8K7plot');
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   var cSol = {};
   var cSol = {};
   for(var i in varsToMutate) cSol[varsToMutate[i]] = 1;
   for(var i in varsToMutate) cSol[varsToMutate[i]] = 1;
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   cSol.v5_K5 = orgC.v5/orgC.K5;
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   //cSol.v5_K5 = orgC.v5/orgC.K5;
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   cSol.v5 = orgC.v5;
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   //cSol.v5 = orgC.v5;
   cSol.k8 = 1000;
   cSol.k8 = 1000;
   cSol.k8_K7 = 1e6;
   cSol.k8_K7 = 1e6;
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   var c = {};
   var c = {};
   for(var i in varsToMutate) c[varsToMutate[i]] = 1;
   for(var i in varsToMutate) c[varsToMutate[i]] = 1;
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   c.v5_K5 = orgC.v5/orgC.K5;
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   //c.v5_K5 = orgC.v5/orgC.K5;
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   c.v5 = orgC.v5;
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   //c.v5 = orgC.v5;
   c.k8 = 1000;
   c.k8 = 1000;
   c.k8_K7 = 1e6;
   c.k8_K7 = 1e6;
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function refreshGraphs() {
function refreshGraphs() {
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   document.getElementById('Meng2004Graph').refresh();
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   //document.getElementById('Meng2004Graph').refresh();
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   document.getElementById('Singh2008Graph').refresh();
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   //document.getElementById('Singh2008Graph').refresh();
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   document.getElementById('Kostal2004fig3BGraph').refresh();
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   //document.getElementById('Kostal2004fig3BGraph').refresh();
   document.getElementById('pSB1A2timeGraph').refresh();
   document.getElementById('pSB1A2timeGraph').refresh();
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   document.getElementById('pArsRRFPtimeGraph').refresh();
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   //document.getElementById('pArsRRFPtimeGraph').refresh();
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   document.getElementById('Kostal2004fig3AGraph').refresh();
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   //document.getElementById('Kostal2004fig3AGraph').refresh();
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   document.getElementById('pSB1A2conGraph').refresh();
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   //document.getElementById('pSB1A2conGraph').refresh();
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   document.getElementById('pArsRRFPconGraph').refresh();
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   //document.getElementById('pArsRRFPconGraph').refresh();
}
}
function showOutputs(mode,E,c,dc) {
function showOutputs(mode,E,c,dc) {
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   plotMin(v5K5plot,mutateFuncs.v5(c),mutateFuncs.K5(c),E);
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   //plotMin(v5K5plot,mutateFuncs.v5(c),mutateFuncs.K5(c),E);
   plotMin(k8K7plot,mutateFuncs.k8(c),mutateFuncs.K7(c),E);
   plotMin(k8K7plot,mutateFuncs.k8(c),mutateFuncs.K7(c),E);
   for(var a in c) {
   for(var a in c) {
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{{GraphHeader}}
{{GraphHeader}}
{|
{|
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|{{graph|Team:Groningen/Graphs/Characterization/GlpF|id=Meng2004Graph}}
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<!--|{{graph|Team:Groningen/Graphs/Characterization/GlpF|id=Meng2004Graph}}
|{{graph|Team:Groningen/Graphs/Characterization/Singh2008|id=Singh2008Graph}}
|{{graph|Team:Groningen/Graphs/Characterization/Singh2008|id=Singh2008Graph}}
|-
|-
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|{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3B|id=Kostal2004fig3BGraph}}
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|{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3B|id=Kostal2004fig3BGraph}}-->
|{{graph|Team:Groningen/Graphs/Characterization/pSB1A2time|id=pSB1A2timeGraph}}
|{{graph|Team:Groningen/Graphs/Characterization/pSB1A2time|id=pSB1A2timeGraph}}
-
|-
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<!--|-
|{{graph|Team:Groningen/Graphs/Characterization/pArsRRFPtime|id=pArsRRFPtimeGraph}}
|{{graph|Team:Groningen/Graphs/Characterization/pArsRRFPtime|id=pArsRRFPtimeGraph}}
|{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3A|id=Kostal2004fig3AGraph}}
|{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3A|id=Kostal2004fig3AGraph}}
|-
|-
|{{graph|Team:Groningen/Graphs/Characterization/pSB1A2con|id=pSB1A2conGraph}}
|{{graph|Team:Groningen/Graphs/Characterization/pSB1A2con|id=pSB1A2conGraph}}
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|{{graph|Team:Groningen/Graphs/Characterization/pArsRRFPcon|id=pArsRRFPconGraph}}
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|{{graph|Team:Groningen/Graphs/Characterization/pArsRRFPcon|id=pArsRRFPconGraph}}-->
|}
|}
<!-- Don't forget to update the refreshGraphs function above! -->
<!-- Don't forget to update the refreshGraphs function above! -->

Revision as of 18:31, 15 October 2009

Igemhomelogo.png

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TODO: Talk about the devices we have and in what way we want to characterize them.

Uptake measurements

Sampling scheme
Time (min)
0 10 20 40 60
As(III)exT(0)
(µM) 		0 x
10 x x x x x
20 x
50 x
100 x

To efficiently look at both time and concentration dependent processes we took samples as in the table on the right. Below we list all results, which have been used for fitting all necessary parameters.

TODO: List results. Take conversion from nmol/mg and mg/ml to µM and Vc/Vs into account.

best cur gradient solved
v5/K5
v5
K5
k8/K7
k8
K7
tauBbeta4
tauB
beta4
tauR
beta1
tauFbetaF
tauF
betaF
tauKbetaK
tauK
betaK
tauGbeta5
tauG
beta5
ars2T
E

Loading graph...
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