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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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{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, | ||
| Line 162: | Line 162: | ||
{constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},AsT:20e-6, | {constants:{Vc:0.006666667,Vs:(1-0.006666667),pro:0,ars2T:0,proK:16.605e-9},AsT:20e-6, | ||
data:{AsinT:[2.25e-4,3.47e-4,4.19e-4,3.93e-4,4.19e-4,4.82e-4,4.82e-4,4.95e-4], | data:{AsinT:[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:[582,1212,1890,2514,3144,3828,4260,6036]}}, | + | time:[582,1212,1890,2514,3144,3828,4260,6036]/*}}, |
pSB1A2con: // concentration mode this is our first icps measerment wild type | pSB1A2con: // concentration mode this is our first icps measerment wild type | ||
{constants:{Vc:0.000808081,Vs:(1-0.000808081),ars2T:0},time:Infinity, | {constants:{Vc:0.000808081,Vs:(1-0.000808081),ars2T:0},time:Infinity, | ||
data:{AsinT:[0.167289553e-6,0.185086314e-6,0.398647446e-6,0.473393842e-6], | data:{AsinT:[0.167289553e-6,0.185086314e-6,0.398647446e-6,0.473393842e-6], | ||
| - | AsT:[10e-6,20e-6,50e-6,100e-6]}}, | + | AsT:[10e-6,20e-6,50e-6,100e-6]}}, |
pSB1A2time: // concentration mode this is our first icps measerment wild type | pSB1A2time: // concentration mode this is our first icps measerment wild type | ||
{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:[180,600,1200,2400,3600]}}, | time:[180,600,1200,2400,3600]}}, | ||
| - | pArsRRFPcon: /* here the cell only contains extra RFP behind the the extra ArsR promotors. | + | 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:[180,600,1200,2400,3600]}}}; | + | 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 15:49, 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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