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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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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, | ||
1111.23287671233e-6,1229.58904109589e-6], | 1111.23287671233e-6,1229.58904109589e-6], | ||
| - | time:[60,600,1200,2400,3600]}}, | + | time:[60,600,1200,2400,3600]}}, |
Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3) | Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3) | ||
{constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0,proF:16.605e-9},AsT:0.467154987e-6, | {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0,proF:16.605e-9},AsT:0.467154987e-6, | ||
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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]*/ | + | /*[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]*/}}, |
| - | + | /*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], | ||
| - | time:[44928,83520,132192,171036]}},*/ | + | time:[44928,83520,132192,171036]}},*/ |
Kostal2004fig3A: // fig 3A | Kostal2004fig3A: // fig 3A | ||
{constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},time:Infinity, | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},time:Infinity, | ||
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{constants:{Vc:0.002320346,Vs:(1-0.002320346),ars2T:0},AsT:10e-6, | {constants:{Vc:0.002320346,Vs:(1-0.002320346),ars2T:0},AsT:10e-6, | ||
data:{AsinT:[0.153306384e-6,0.194188086e-6,0.265731066e-6,0.306612768e-6,0.480360003e-6], | data:{AsinT:[0.153306384e-6,0.194188086e-6,0.265731066e-6,0.306612768e-6,0.480360003e-6], | ||
| - | time:[ | + | time:[180,600,1200,2400,3600]}}, |
| - | pArsRRFPcon: | + | pArsRRFPcon: /* here the cell only contains extra RFP behind the the extra ArsR promotors. |
| - | We incorporate this in our model by pretending RFP=GVP (1st icps)*/ | + | We incorporate this in our model by pretending RFP=GVP (1st icps)*/ |
{constants:{Vc:0.001272727,Vs:(1-0.001272727)},time:Infinity, | {constants:{Vc:0.001272727,Vs:(1-0.001272727)},time:Infinity, | ||
data:{AsinT:[0.173785371e-6,0.353176722e-6,0.369994661e-6,0.437266418e-6], | data:{AsinT:[0.173785371e-6,0.353176722e-6,0.369994661e-6,0.437266418e-6], | ||
AsT:[10e-6,20e-6,50e-6,100e-6]}}, | AsT:[10e-6,20e-6,50e-6,100e-6]}}, | ||
| - | pArsRRFPtime: | + | pArsRRFPtime: /* here the cell only contains extra RFP behind the the extra ArsR promotors. |
| - | We incorporate this in our model by pretending RFP=GVP (1st icps)*/ | + | We incorporate this in our model by pretending RFP=GVP (1st icps)*/ |
{constants:{Vc:0.003333333,Vs:(1-0.003333333)},AsT:10e-6, | {constants:{Vc:0.003333333,Vs:(1-0.003333333)},AsT:10e-6, | ||
data:{AsinT:[0.176187934e-6,0.308328884e-6,0.102776295e-6,0.293646556e-6,0.455152162e-6], | data:{AsinT:[0.176187934e-6,0.308328884e-6,0.102776295e-6,0.293646556e-6,0.455152162e-6], | ||
| - | time:[ | + | time:[180,600,1200,2400,3600]}}}; |
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']; | ||
Revision as of 15:38, 12 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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