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Team:Groningen/Modelling/Characterization
From 2009.igem.org
(Difference between revisions)
(Simulated annealing) |
(Some tweaks to simulated annealing.) |
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| Line 60: | Line 60: | ||
!best | !best | ||
!cur | !cur | ||
| + | !solved | ||
|- | |- | ||
|v5 | |v5 | ||
|id="v5"| | |id="v5"| | ||
|id="v5cur"| | |id="v5cur"| | ||
| + | |id="v5sol"| | ||
|- | |- | ||
|K5 | |K5 | ||
|id="K5"| | |id="K5"| | ||
|id="K5cur"| | |id="K5cur"| | ||
| + | |id="K5sol"| | ||
|- | |- | ||
|E | |E | ||
|id="E"| | |id="E"| | ||
|id="Ecur"| | |id="Ecur"| | ||
| + | |id="Esol"| | ||
|} | |} | ||
<html> | <html> | ||
| Line 100: | Line 104: | ||
var varsToMutate = ['v5','K5']; | var varsToMutate = ['v5','K5']; | ||
| + | var mutateDeps = {v5: ['K5']}; | ||
function mutate(c) { | function mutate(c) { | ||
var vn = varsToMutate[Math.floor(Math.random()*varsToMutate.length)]; | var vn = varsToMutate[Math.floor(Math.random()*varsToMutate.length)]; | ||
var nc = {}; | var nc = {}; | ||
for(var a in c) nc[a] = c[a]; | for(var a in c) nc[a] = c[a]; | ||
| - | + | ||
| - | + | // Mutate | |
| - | + | var factor = 2-Math.exp(-Math.random()); | |
| - | + | if (Math.random()<0.5) { | |
| + | factor = 1 /(2-Math.exp(-Math.random())); | ||
} | } | ||
| + | nc[vn] *= factor; | ||
| + | for(var i in mutateDeps[vn]) nc[mutateDeps[vn][i]] *= factor; | ||
return nc; | return nc; | ||
} | } | ||
| Line 114: | Line 122: | ||
function fitConstants() { | function fitConstants() { | ||
var c = arsenicModelConstants(); | var c = arsenicModelConstants(); | ||
| + | setOutput('v5sol',c.v5); | ||
| + | setOutput('K5sol',c.K5); | ||
| + | setOutput('Esol',computeCost(c,experiments)); | ||
c.v5 = 1e-3; | c.v5 = 1e-3; | ||
c.K5 = 1e-3; | c.K5 = 1e-3; | ||
Revision as of 14:44, 28 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 | solved | |
|---|---|---|---|
| v5 | |||
| K5 | |||
| E |
