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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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(Now also support for experiments measuring equilibrium uptake) |
m (Fix for AsT on x-axis) |
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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: | + | 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, | ||
| Line 150: | Line 150: | ||
0.361791516e-6,0.332907991e-6,0.320748614e-6], | 0.361791516e-6,0.332907991e-6,0.320748614e-6], | ||
time:[60,300,600,1200,1800,3600] | time:[60,300,600,1200,1800,3600] | ||
| - | + | */ /*[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]*/ /*}}, | |
| - | + | Kostal2004: // fig 2C | |
| - | {constants:{ | + | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},AsT:10e-6, |
| - | data:{AsinT:[ | + | data:{AsinT:[159.39e-6,491.7e-6,679.8e-6,742.5], |
| + | time:[44928,83520,132192,171036]}},*/ | ||
| + | Kostal2004: // fig 3A | ||
| + | {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], | ||
| + | AsT:[0.2086e-6,0.4742e-6,1.0386e-6,2.4854e-6,16.7308e-6,45.8816e-6,95.6726e-6]}}}; | ||
var varsToMutate = ['v5_K5','v5','k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4']; | var varsToMutate = ['v5_K5','v5','k8_K7','k8','tauBbeta4','beta4','tauR_tauB','beta1_beta4']; | ||
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for(var xn in e[i].data) { | for(var xn in e[i].data) { | ||
if (xn=='AsT') continue; | if (xn=='AsT') continue; | ||
| - | curcost += Math.pow((e[i].data[xn][j]-xt[xn])/avgv,2); | + | curcost += Math.pow((e[i].data[xn][j]-xt[xn])/avgv[xn],2); |
n++; | n++; | ||
} | } | ||
Revision as of 12:26, 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"
