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Team:Groningen/Modelling/Characterization
From 2009.igem.org
(Difference between revisions)
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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 = { | + | 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 | + | /*Kostal2004: // fig 2C |
{constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},AsT:10e-6, | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},AsT:10e-6, | ||
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], | ||
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{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], | ||
| - | AsT:[0. | + | AsT:[0.4e-6,1e-6,2e-6,5e-6,20e-6,50e-6,100e-6]}}, |
| + | Kostal2004fig3B: //fig 3B | ||
| + | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0},AsT:20e-6, | ||
| + | data:{AsinT:[0,2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4], | ||
| + | time:[0,582,1212,1890,2514,3144,3828,4260,6036]}}}; | ||
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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document.getElementById('Singh2008Graph').refresh(); | document.getElementById('Singh2008Graph').refresh(); | ||
document.getElementById('Kostal2004fig3AGraph').refresh(); | document.getElementById('Kostal2004fig3AGraph').refresh(); | ||
| + | document.getElementById('Kostal2004fig3BGraph').refresh(); | ||
} | } | ||
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|- | |- | ||
|{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3A|id=Kostal2004fig3AGraph}} | |{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3A|id=Kostal2004fig3AGraph}} | ||
| + | |{{graph|Team:Groningen/Graphs/Characterization/Kostal2004fig3B|id=Kostal2004fig3BGraph}} | ||
|} | |} | ||
<!-- Don't forget to update the refreshGraphs function above! --> | <!-- Don't forget to update the refreshGraphs function above! --> | ||
Revision as of 14:33, 6 October 2009
 |
|---|
- 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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