Team:Groningen/Modelling/Characterization

From 2009.igem.org

(Difference between revisions)
(Starting to write fitting function.)
m (Make use of timekey.)
Line 62: Line 62:
<script type="text/javascript">
<script type="text/javascript">
var experiments = [{constants:{Vc:0.0073e-3,Vs:(1.1-0.0073)*1e-3,beta4:0},AsT:10e-6*1e-3,
var experiments = [{constants:{Vc:0.0073e-3,Vs:(1.1-0.0073)*1e-3,beta4:0},AsT:10e-6*1e-3,
-
                     AsinT:{1:101.917808219178,10:394.520547945205,20:723.287671232877,
+
                     AsinT:[101.917808219178,394.520547945205,723.287671232877,
-
                        40:1111.23287671233,60:1229.58904109589}}];
+
                          1111.23287671233,1229.58904109589],
 +
                    time:[1,10,20,40,60]}];
function computeCost(c,e) {
function computeCost(c,e) {
   var cost = 0, n = 0, x0, xt, times;
   var cost = 0, n = 0, x0, xt, times;
   for(var i in e) {
   for(var i in e) {
 +
    alert("Experiment "+i);
     var nc = {};
     var nc = {};
     for(var a in c) nc[a] = c[a];
     for(var a in c) nc[a] = c[a];
     for(var a in e[i].constants) nc[a] = e[i].constants[a];
     for(var a in e[i].constants) nc[a] = e[i].constants[a];
     times = [];
     times = [];
-
     for(var t in e[i].AsinT) times.push(t);
+
     for(var t=0; t<e[i].time.length; t++) times.push(60*e[i].time[t]);
 +
    alert("Times "+times);
     x0 = arsenicModelInitialization(nc,e[i].AsT);
     x0 = arsenicModelInitialization(nc,e[i].AsT);
 +
    alert("x0.AsinT "+x0.AsinT);
     xt = simulate(x0,times,function(t,d){return arsenicModelGradient(nc,d);});
     xt = simulate(x0,times,function(t,d){return arsenicModelGradient(nc,d);});
-
     for(var j in xt.time) {
+
    alert("Ready simulating");
-
       if (e[i].AsinT[xt.time[j]]) {
+
     for(var j in xt.timeKey) {
-
        cost += Math.pow(e[i].AsinT[xt.time[j]]-xt.AsinT[j],2);
+
       cost += Math.pow(e[i].AsinT[j]-xt.AsinT[xt.timeKey[j]],2);
-
        n++;
+
      n++;
-
      }
+
     }
     }
   }
   }

Revision as of 13:45, 28 September 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.

Retrieved from "http://2009.igem.org/Team:Groningen/Modelling/Characterization"