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Team:Groningen/Modelling/Characterization
From 2009.igem.org
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(Added a plot of the Meng2004 fit.) |
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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, | ||
AsinT:[101.917808219178e-6,394.520547945205e-6,723.287671232877e-6, | 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]}, | ||
| - | {constants:{Vc:(0.004545455 | + | Singh2008: // We assume 5g/L wet cells were used... (at 1100kg/m^3) |
| - | AsinT:[10.49961532e-6 | + | {constants:{Vc:(0.004545455),Vs:(1-(0.004545455)),pro:0,ars2T:0},AsT:0.467154987e-6, |
| - | 29.40009211e-6 | + | AsinT:[10.49961532e-6,16.62049351e-6,19.44416512e-6,23.07460003e-6, |
| + | 29.40009211e-6,32.06299566e-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]*/}}; |
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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// Go through all experiments | // Go through all experiments | ||
| - | var cost = 0, x0, xt, times; | + | var cost = 0, weight = 0, x0, xt, times; |
for(var i in e) { | for(var i in e) { | ||
// Set up constants for this experiment | // Set up constants for this experiment | ||
| Line 185: | Line 187: | ||
} | } | ||
cost += Math.sqrt(curcost/xt.timeKey.length); // Compute the square root of the average of the squares (RMS) | cost += Math.sqrt(curcost/xt.timeKey.length); // Compute the square root of the average of the squares (RMS) | ||
| + | weight++; | ||
// Set last solution | // Set last solution | ||
e[i].solution = {'cost':curcost, 'xt':xt}; | e[i].solution = {'cost':curcost, 'xt':xt}; | ||
} | } | ||
| - | return cost/ | + | return cost/weight; // Take the average of the RMS values for all graphs, making it "easier" to disregard certain experiments in favour of the rest. |
} | } | ||
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// Show initial situation | // Show initial situation | ||
| - | |||
showOutputs('cur',E,c,dc); | showOutputs('cur',E,c,dc); | ||
showOutputs('',EBest,cBest); | showOutputs('',EBest,cBest); | ||
| + | for(var i in experiments) experiments[i].bestSolution = experiments[i].solution; | ||
| + | document.getElementById('Meng2004Graph').refresh(); | ||
// Set up iteration | // Set up iteration | ||
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cBest = cNew; | cBest = cNew; | ||
EBest = ENew; | EBest = ENew; | ||
| - | |||
showOutputs('',EBest,cBest); | showOutputs('',EBest,cBest); | ||
| + | for(var i in experiments) experiments[i].bestSolution = experiments[i].solution; | ||
| + | document.getElementById('Meng2004Graph').refresh(); | ||
} | } | ||
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</html> | </html> | ||
{{GraphHeader}} | {{GraphHeader}} | ||
| - | {{graph|Team:Groningen/Graphs/Characterization/GlpF}} | + | {{graph|Team:Groningen/Graphs/Characterization/GlpF|id=Meng2004Graph}} |
Revision as of 10:47, 5 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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Loading graph...
