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Team:Groningen/Modelling/Characterization
From 2009.igem.org
(Difference between revisions)
(Use relative errors instead of absolute errors.) |
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| Line 80: | Line 80: | ||
|id="K5curgradient"| | |id="K5curgradient"| | ||
|id="K5sol"| | |id="K5sol"| | ||
| + | |- | ||
| + | |k8/K7 | ||
| + | |id="k8K7"| | ||
| + | |id="k8K7cur"| | ||
| + | |id="k8K7curgradient"| | ||
| + | |id="k8K7sol"| | ||
| + | |- | ||
| + | |k8 | ||
| + | |id="k8"| | ||
| + | |id="k8cur"| | ||
| + | |id="k8curgradient"| | ||
| + | |id="k8sol"| | ||
| + | |- | ||
| + | |K7 | ||
| + | |id="K7"| | ||
| + | |id="K7cur"| | ||
| + | |id="K7curgradient"| | ||
| + | |id="K7sol"| | ||
|- | |- | ||
|E | |E | ||
| Line 101: | Line 119: | ||
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]}]; | ||
| - | var varsToMutate = ['v5K5','K5']; | + | var varsToMutate = ['v5K5','K5','k8K7','K7']; |
var mutateFuncs = {v5: function(v){return v.v5K5*v.K5;}, | var mutateFuncs = {v5: function(v){return v.v5K5*v.K5;}, | ||
| - | K5: function(v){return v.K5;}}; | + | K5: function(v){return v.K5;}, |
| + | k8: function(v){return v.k8K7*v.K7;}, | ||
| + | K7: function(v){return v.K7;}}; | ||
function computeCost(v,e) { | function computeCost(v,e) { | ||
| Line 152: | Line 172: | ||
setOutput('v5'+mode,mutateFuncs.v5(c)); | setOutput('v5'+mode,mutateFuncs.v5(c)); | ||
setOutput('K5'+mode,mutateFuncs.K5(c)); | setOutput('K5'+mode,mutateFuncs.K5(c)); | ||
| + | setOutput('k8K7'+mode,mutateFuncs.k8(c)/mutateFuncs.K7(c)); | ||
| + | setOutput('k8'+mode,mutateFuncs.k8(c)); | ||
| + | setOutput('K7'+mode,mutateFuncs.K7(c)); | ||
setOutput('E'+mode,computeCost(c,experiments)); | setOutput('E'+mode,computeCost(c,experiments)); | ||
if (dc!=undefined) { | if (dc!=undefined) { | ||
| Line 157: | Line 180: | ||
setOutput('v5'+mode+'gradient',dc.v5K5*c.K5-dc.K5*c.v5K5); | setOutput('v5'+mode+'gradient',dc.v5K5*c.K5-dc.K5*c.v5K5); | ||
setOutput('K5'+mode+'gradient',dc.K5); | setOutput('K5'+mode+'gradient',dc.K5); | ||
| + | setOutput('k8K7'+mode+'gradient',dc.k8K7); | ||
| + | setOutput('k8'+mode+'gradient',dc.k8K7*c.K7-dc.K7*c.k8K7); | ||
| + | setOutput('K7'+mode+'gradient',dc.K7); | ||
} | } | ||
} | } | ||
| Line 163: | Line 189: | ||
// Show mathematica solution | // Show mathematica solution | ||
var orgC = arsenicModelConstants(); | var orgC = arsenicModelConstants(); | ||
| - | var cSol = {v5K5 | + | var cSol = {}; |
| + | for(var i in varsToMutate) c[varsToMutate[i]] = 1; | ||
| + | cSol.v5K5 = orgC.v5/orgC.K5; | ||
| + | cSol.K5 = orgC.K5; | ||
showOutputs('sol',computeCost(cSol,experiments),cSol); | showOutputs('sol',computeCost(cSol,experiments),cSol); | ||
Revision as of 11:06, 30 September 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 | ||||
| E |
