Team:Groningen/Modelling/Characterization

From 2009.igem.org

(Difference between revisions)
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                           time:[60,600,1200,2400,3600]}},
                           time:[60,600,1200,2400,3600]}},
                   Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3)
                   Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3)
-
                   {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),beta1:0,pro:0,ars2T:0,
+
                   {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0,
-
                               proF:1.6605e-9,beta4:0,ars1T:0},AsT:0.467154987e-6,
+
                               proF:1.6605e-9},AsT:0.467154987e-6,
                     data:{AsexT:[0.419211538e-6,0.391262322e-6,0.378368845e-6,
                     data:{AsexT:[0.419211538e-6,0.391262322e-6,0.378368845e-6,
                                 0.361791516e-6,0.332907991e-6,0.320748614e-6],
                                 0.361791516e-6,0.332907991e-6,0.320748614e-6],
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                           AsT:[0.4e-6,1e-6,2e-6,5e-6,20e-6,50e-6,100e-6]}},*/
                           AsT:[0.4e-6,1e-6,2e-6,5e-6,20e-6,50e-6,100e-6]}},*/
                   Kostal2004fig3B:  //fig 3B
                   Kostal2004fig3B:  //fig 3B
-
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),beta1:0,ars1T:0,beta4:0,pro:0,ars2T:0,
+
                   {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:1.6605e-9},AsT:20e-6,
-
                                                      proK:1.6605e-9},AsT:20e-6,
+
                     data:{AsinT:[2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4],
                     data:{AsinT:[2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4],
                           time:[582,1212,1890,2514,3144,3828,4260,6036]}},/*
                           time:[582,1212,1890,2514,3144,3828,4260,6036]}},/*
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   cSol.k8 = 1000;
   cSol.k8 = 1000;
   cSol.k8_K7 = 1e6;
   cSol.k8_K7 = 1e6;
-
  cSol.tauBbeta4 = 180000;
+
//  cSol.tauBbeta4 = 180000;
-
  cSol.tauB = 180;
+
//  cSol.tauB = 180;
-
  cSol.beta4 = 1000;
+
//  cSol.beta4 = 1000;
-
  cSol.tauR = 60;
+
//  cSol.tauR = 60;
-
  cSol.beta1 = 1000;
+
//  cSol.beta1 = 1000;
-
  cSol.tauFbetaF = 120000;
+
//  cSol.tauFbetaF = 120000;
-
  cSol.tauF = 60;
+
//  cSol.tauF = 60;
-
  cSol.betaF = 2000;
+
//  cSol.betaF = 2000;
-
  cSol.tauKbetaK = 9240;
+
//  cSol.tauKbetaK = 9240;
-
  cSol.tauK = 60;
+
//  cSol.tauK = 60;
-
  cSol.betaK = 154;
+
//  cSol.betaK = 154;
-
  cSol.tauGbeta5 = 3960;
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//  cSol.tauGbeta5 = 3960;
-
  cSol.tauG = 60;
+
//  cSol.tauG = 60;
-
  cSol.beta5 = 66;
+
//  cSol.beta5 = 66;
   showOutputs('sol',computeCost(cSol,experiments),cSol);
   showOutputs('sol',computeCost(cSol,experiments),cSol);
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   c.k8 = 1000;
   c.k8 = 1000;
   c.k8_K7 = 1e6;
   c.k8_K7 = 1e6;
-
  cSol.tauBbeta4 = 180000;
+
//  cSol.tauBbeta4 = 180000;
-
  cSol.tauB = 180;
+
//  cSol.tauB = 180;
-
  cSol.beta4 = 1000;
+
//  cSol.beta4 = 1000;
-
  cSol.tauR = 60;
+
//  cSol.tauR = 60;
-
  cSol.beta1 = 1000;
+
//  cSol.beta1 = 1000;
-
  cSol.tauFbetaF = 120000;
+
//  cSol.tauFbetaF = 120000;
-
  cSol.tauF = 60;
+
//  cSol.tauF = 60;
-
  cSol.betaF = 2000;
+
//  cSol.betaF = 2000;
-
  cSol.tauKbetaK = 9240;
+
//  cSol.tauKbetaK = 9240;
-
  cSol.tauK = 60;
+
//  cSol.tauK = 60;
-
  cSol.betaK = 154;
+
//  cSol.betaK = 154;
-
  cSol.tauGbeta5 = 3960;
+
//  cSol.tauGbeta5 = 3960;
-
  cSol.tauG = 60;
+
//  cSol.tauG = 60;
-
  cSol.beta5 = 66;  var dc = {};
+
//  cSol.beta5 = 66;  var dc = {};
   for(var a in c) dc[a] = 0;
   for(var a in c) dc[a] = 0;
   var E = computeCost(c,experiments);
   var E = computeCost(c,experiments);

Revision as of 10:44, 13 October 2009

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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
E

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