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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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|id="beta1curgradient"| | |id="beta1curgradient"| | ||
|id="beta1sol"| | |id="beta1sol"| | ||
| + | |- | ||
| + | |tauFbetaF | ||
| + | |id="tauFbetaF"| | ||
| + | |id="tauFbetaFcur"| | ||
| + | |id="tauFbetaFcurgradient"| | ||
| + | |id="tauFbetaFsol"| | ||
| + | |- | ||
| + | |tauF | ||
| + | |id="tauF"| | ||
| + | |id="tauFcur"| | ||
| + | |id="tauFcurgradient"| | ||
| + | |id="tauFsol"| | ||
| + | |- | ||
| + | |betaF | ||
| + | |id="betaF"| | ||
| + | |id="betaFcur"| | ||
| + | |id="betaFcurgradient"| | ||
| + | |id="betaFsol"| | ||
|- | |- | ||
|E | |E | ||
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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)),beta1:0,pro:0,ars2T:0, | {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),beta1:0,pro:0,ars2T:0, | ||
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data:{AsexT:[0.419211538e-6,0.391262322e-6,0.378368845e-6, | data:{AsexT:[0.419211538e-6,0.391262322e-6,0.378368845e-6, | ||
0.361791516e-6,0.332907991e-6,0.320748614e-6], | 0.361791516e-6,0.332907991e-6,0.320748614e-6], | ||
| - | time:[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]}}, | + | time:[1.127*60,4.993*60,9.986*60,20.159*60,30.181*60,60.035*60]/*}}, |
Kostal2004fig3A: // fig 3A | Kostal2004fig3A: // fig 3A | ||
{constants:{Vc:0.006666667,Vs:(1-0.006666667),beta4:0,pro:0,ars2T:0},time:Infinity, | {constants:{Vc:0.006666667,Vs:(1-0.006666667),beta4:0,pro:0,ars2T:0},time:Infinity, | ||
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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','tauFbetaF','betaF']; |
var mutateFuncs = {v5: function(v){return v.v5;}, | var mutateFuncs = {v5: function(v){return v.v5;}, | ||
K5: function(v){return v.v5/v.v5_K5;}, | K5: function(v){return v.v5/v.v5_K5;}, | ||
| Line 187: | Line 205: | ||
tauR: function(v){return v.tauR_tauB*v.tauBbeta4/v.beta4;}, | tauR: function(v){return v.tauR_tauB*v.tauBbeta4/v.beta4;}, | ||
beta4: function(v){return v.beta4;}, | beta4: function(v){return v.beta4;}, | ||
| - | beta1: function(v){return v.beta4*v.beta1_beta4;}}; | + | beta1: function(v){return v.beta4*v.beta1_beta4;}, |
| + | tauF: function(v){return v.tauFbetaF/v.betaF;}, | ||
| + | betaF: function(v){return v.betaF;}}; | ||
function computeCost(v,e) { | function computeCost(v,e) { | ||
Revision as of 18:16, 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 | ||||
| tauFbetaF | ||||
| tauF | ||||
| betaF | ||||
| E |
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