Team:Groningen/Modelling/Characterization

From 2009.igem.org

(Difference between revisions)
(Undo revision 80257 by Kbover (Talk))
m
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|id="K7curgradient"|
|id="K7curgradient"|
|id="K7sol"|
|id="K7sol"|
 +
|-
 +
|tauBbeta4
 +
|id="tauBbeta4"|
 +
|id="tauBbeta4cur"|
 +
|id="tauBbeta4curgradient"|
 +
|id="tauBbeta4sol"|
 +
|-
 +
|tauB
 +
|id="tauB"|
 +
|id="tauBcur"|
 +
|id="tauBcurgradient"|
 +
|id="tauBsol"|
 +
|-
 +
|beta4
 +
|id="beta4"|
 +
|id="beta4cur"|
 +
|id="beta4curgradient"|
 +
|id="beta4sol"|
|-
|-
|E
|E
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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 = [{constants:{Vc:0.0073,Vs:(1.1-0.0073),beta4:0},AsT:10e-6,
+
var experiments = [{constants:{Vc:0.0073,Vs:(1.1-0.0073),pro:0,ars2T:0},AsT:10e-6,
                     AsinT:[101.917808219178e-6,394.520547945205e-6,723.287671232877e-6,
                     AsinT:[101.917808219178e-6,394.520547945205e-6,723.287671232877e-6,
                           1111.23287671233e-6,1229.58904109589e-6],
                           1111.23287671233e-6,1229.58904109589e-6],
                     time:[60,600,1200,2400,3600]},
                     time:[60,600,1200,2400,3600]},
-
                   {constants:{Vc:0.004545455,Vs:(1-0.004545455)},AsT:0.467154987e-6,
+
                   {constants:{Vc:0.004545455,Vs:(1-0.004545455),pro:0,ars2T:0},AsT:0.467154987e-6,
                     AsinT:[10.49961532e-6,16.62049351e-6,19.44416512e-6,23.07460003e-6,
                     AsinT:[10.49961532e-6,16.62049351e-6,19.44416512e-6,23.07460003e-6,
                             29.40009211e-6,32.06299566e-6],
                             29.40009211e-6,32.06299566e-6],
                     time:[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]}];   
                     time:[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]}];   
-
var varsToMutate = ['v5K5','K5','k8K7','K7'];
+
var varsToMutate = ['v5K5','K5','k8K7','K7','tauBbeta4','beta4'];
var mutateFuncs = {v5: function(v){return v.v5K5*v.K5;},
var mutateFuncs = {v5: function(v){return v.v5K5*v.K5;},
                   K5: function(v){return v.K5;},
                   K5: function(v){return v.K5;},
                   k8: function(v){return v.k8K7*v.K7;},
                   k8: function(v){return v.k8K7*v.K7;},
-
                   K7: function(v){return v.K7;}};
+
                   K7: function(v){return v.K7;},
 +
                  tauB: function(v){return v.tauBbeta4/v.beta4;},
 +
                  beta4: function(v){return v.beta4;}};
function computeCost(v,e) {
function computeCost(v,e) {
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   setOutput('k8'+mode,mutateFuncs.k8(c));
   setOutput('k8'+mode,mutateFuncs.k8(c));
   setOutput('K7'+mode,mutateFuncs.K7(c));
   setOutput('K7'+mode,mutateFuncs.K7(c));
-
   setOutput('E'+mode,computeCost(c,experiments));
+
   setOutput('tauBbeta4'+mode,mutateFuncs.tauB(c)/mutateFuncs.beta4(c));
 +
  setOutput('tauB'+mode,mutateFuncs.tauB(c));
 +
  setOutput('beta4'+mode,mutateFuncs.beta4(c));
 +
  setOutput('E'+mode,E);
   if (dc!=undefined) {
   if (dc!=undefined) {
     setOutput('v5K5'+mode+'gradient',dc.v5K5);
     setOutput('v5K5'+mode+'gradient',dc.v5K5);
-
     setOutput('v5'+mode+'gradient',dc.v5K5*c.K5-dc.K5*c.v5K5);
+
     setOutput('v5'+mode+'gradient',dc.v5K5*c.K5+dc.K5*c.v5K5);
     setOutput('K5'+mode+'gradient',dc.K5);
     setOutput('K5'+mode+'gradient',dc.K5);
     setOutput('k8K7'+mode+'gradient',dc.k8K7);
     setOutput('k8K7'+mode+'gradient',dc.k8K7);
-
     setOutput('k8'+mode+'gradient',dc.k8K7*c.K7-dc.K7*c.k8K7);
+
     setOutput('k8'+mode+'gradient',dc.k8K7*c.K7+dc.K7*c.k8K7);
     setOutput('K7'+mode+'gradient',dc.K7);
     setOutput('K7'+mode+'gradient',dc.K7);
 +
    setOutput('tauBbeta4'+mode+'gradient',dc.tauBbeta4);
 +
    setOutput('tauB'+mode+'gradient',(dc.tauBbeta4*c.beta4-dc.beta4*c.tauBbeta4)/Math.pow(c.beta4,2));
 +
    setOutput('beta4'+mode+'gradient',dc.beta4);
   }
   }
}
}

Revision as of 08:31, 1 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
E
Retrieved from "http://2009.igem.org/Team:Groningen/Modelling/Characterization"