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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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data:{AsinT:[159.39e-6,491.7e-6,679.8e-6,742.5], | data:{AsinT:[159.39e-6,491.7e-6,679.8e-6,742.5], | ||
time:[44928,83520,132192,171036]}},*/ | time:[44928,83520,132192,171036]}},*/ | ||
| - | + | Kostal2004fig3A: // fig 3A | |
{constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},time:Infinity, | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},time:Infinity, | ||
data:{AsinT:[28.71e-6,78.87e-6,144.21e-6,377.19e-6,490.38e-6,617.76e-6,649.11e-6], | data:{AsinT:[28.71e-6,78.87e-6,144.21e-6,377.19e-6,490.38e-6,617.76e-6,649.11e-6], | ||
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// Set last solution | // Set last solution | ||
| - | e[i].solution = {'cost':curcost, 'xt':xt}; | + | e[i].solution = {'cost':Math.sqrt(curcost/n), 'xt':xt}; |
} else if (e[i].time==Infinity) { // Vary AsT, with equilibrium | } else if (e[i].time==Infinity) { // Vary AsT, with equilibrium | ||
var avgv = {}; | var avgv = {}; | ||
| Line 212: | Line 212: | ||
avgv[xn] /= e[i].data[xn].length; | avgv[xn] /= e[i].data[xn].length; | ||
} | } | ||
| + | e[i].solution = {'xt':{'AsT':[]}}; | ||
var curcost = 0, n = 0; | var curcost = 0, n = 0; | ||
for(var j in e[i].data.AsT) { | for(var j in e[i].data.AsT) { | ||
// Simulate | // Simulate | ||
xt = arsenicModelEquilibrium(nc,e[i].data.AsT[j]); | xt = arsenicModelEquilibrium(nc,e[i].data.AsT[j]); | ||
| + | e[i].solution.xt.AsT[j] = e[i].data.AsT[j]; | ||
| + | |||
| + | // Fill solution | ||
| + | for(var xn in xt) { | ||
| + | if (e[i].solution.xt[xn]==undefined) e[i].solution.xt[xn] = []; | ||
| + | e[i].solution.xt[xn][j] = xt[xn]; | ||
| + | } | ||
// Sum (squares of) errors, divided by the average value | // Sum (squares of) errors, divided by the average value | ||
| Line 226: | Line 234: | ||
cost += Math.sqrt(curcost/n); // Compute the square root of the average of the squares (RMS) | cost += Math.sqrt(curcost/n); // Compute the square root of the average of the squares (RMS) | ||
weight++; | weight++; | ||
| + | e[i].solution.cost = Math.sqrt(curcost/n); | ||
} | } | ||
} | } | ||
Revision as of 12:55, 6 October 2009
[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]
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- Modelling
- DetailedModel
- Characterization
- Downloads
TODO: Talk about the devices we have and in what way we want to characterize them.
Uptake measurements
| 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 | ||||
| E |
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Retrieved from "http://2009.igem.org/Team:Groningen/Modelling/Characterization"
