Team:Oxford/notebook

From 2014.igem.org

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[[File:Model 1.png|900px|thumb|left|An example of the model's output]]
[[File:Model 1.png|900px|thumb|left|An example of the model's output]]
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<h2>[DCM] calibration for solution-vapour equilibration</h2>
 +
<p>Testing the tolerance of E-coli and Pseudomonas strains to various concentrations of DCM (0mM, 5mM, 10mM, 20mM), the 15 mL falcon tube-contained system is modeled as a real binary solution/ideal gas, based on literature solubility data<sup>1</sup>, confirming negligible [DCM] deviation:</p></div>
 +
 +
<img src="http://latex.codecogs.com/gif.latex?p_{i}=c*k^{\Theta&space;}e^{\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}(\frac{1}{T}-\frac{1}{298.15K})}" title="p_{i}=c*k^{\Theta }e^{\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}(\frac{1}{T}-\frac{1}{298.15K})}" /><br>
 +
 +
 +
<img src="http://latex.codecogs.com/gif.latex?k^\Theta=3.9*10^{-6}&space;\:&space;mol&space;\:&space;kg^{-1}&space;Pa^{-1},&space;\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}=&space;3900&space;\:K" title="k^\Theta=3.9*10^{-6} \: mol \: kg^{-1} Pa^{-1}, \frac{\mathrm{d} lnk}{\mathrm{d} 1/T}= 3900 \:K" />
 +
 +
<p class="p1"><br></p>
 +
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    td.td12 {width: 93.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
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    td.td13 {width: 81.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
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    td.td15 {width: 58.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
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    td.td17 {width: 69.0px; height: 12.0px; background-color: #64b2df; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
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    td.td18 {width: 50.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td19 {width: 43.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
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    td.td20 {width: 63.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td21 {width: 69.0px; height: 11.0px; background-color: #9ce15a; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td22 {width: 93.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td23 {width: 81.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td24 {width: 59.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td25 {width: 58.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td26 {width: 80.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td27 {width: 69.0px; height: 11.0px; background-color: #64b2df; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td28 {width: 50.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td29 {width: 43.0px; height: 11.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}
 +
    td.td30 {width: 69.0px; height: 12.0px; border-style: solid; border-width: 1.0px 1.0px 1.0px 1.0px; border-color: #000000 #000000 #000000 #000000; padding: 4.0px 4.0px 4.0px 4.0px}">
 +
  <tbody>
 +
    <tr>
 +
      <td valign="top" class="td1">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td2">
 +
        <p class="p2"><span class="s1">V(DCM)</span><span class="s2"><sub> </sub></span><span class="s1">added (± 5E-4) /ml</span></p>
 +
      </td>
 +
      <td valign="top" class="td3">
 +
        <p class="p2"><span class="s1">n(DCM)</span><span class="s2"><sub>(l)</sub></span><span class="s1"> unadjusted (± 8E-6) /mol</span></p>
 +
      </td>
 +
      <td valign="top" class="td4">
 +
        <p class="p2"><span class="s1">[DCM] unadjusted (± 2E-3) /M</span></p>
 +
      </td>
 +
      <td valign="top" class="td5">
 +
        <p class="p2"><span class="s1">p(DCM)<span class="Apple-converted-space"> </span></span></p>
 +
        <p class="p2"><span class="s1">(± 4E-2) /kPa</span></p>
 +
      </td>
 +
      <td valign="top" class="td6">
 +
        <p class="p2"><span class="s1">n(DCM)</span><span class="s2"><sub>(g)</sub></span></p>
 +
        <p class="p2"><span class="s1">(± 4E-7) /mol</span></p>
 +
      </td>
 +
      <td valign="top" class="td7">
 +
        <p class="p2"><span class="s1">n(DCM)</span><span class="s2"><sub>(l)</sub></span><span class="s1"> (± 9E-6) adjusted /mol</span></p>
 +
      </td>
 +
      <td valign="top" class="td2">
 +
        <p class="p2"><span class="s1">[DCM] adjusted<span class="Apple-converted-space"> </span></span></p>
 +
        <p class="p2"><span class="s1">(± 2E-3) /M</span></p>
 +
      </td>
 +
      <td valign="top" class="td8">
 +
        <p class="p2"><span class="s1">Δ[DCM] /M</span></p>
 +
      </td>
 +
      <td valign="top" class="td9">
 +
        <p class="p2"><span class="s1">[DCM] % deviation</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td10">
 +
        <p class="p2"><span class="s1"><b>(30°C, 5mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td11">
 +
        <p class="p3"><span class="s1">1.6E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td12">
 +
        <p class="p3"><span class="s1">2.5E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td13">
 +
        <p class="p3"><span class="s1">5.0E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td14">
 +
        <p class="p3"><span class="s1">6.2E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td15">
 +
        <p class="p3"><span class="s1">1.6E-08</span></p>
 +
      </td>
 +
      <td valign="top" class="td16">
 +
        <p class="p3"><span class="s1">2.5E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td17">
 +
        <p class="p3"><span class="s1"><b>5.0E-03</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td18">
 +
        <p class="p3"><span class="s1">3.1E-06</span></p>
 +
      </td>
 +
      <td valign="top" class="td19">
 +
        <p class="p3"><span class="s1">6.3E-02</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td20">
 +
        <p class="p2"><span class="s1"><b>(30°C, 10mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td21">
 +
        <p class="p3"><span class="s1">3.2E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td22">
 +
        <p class="p3"><span class="s1">5.0E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td23">
 +
        <p class="p3"><span class="s1">1.0E-02</span></p>
 +
      </td>
 +
      <td valign="top" class="td24">
 +
        <p class="p3"><span class="s1">3.1E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td25">
 +
        <p class="p3"><span class="s1">7.9E-09</span></p>
 +
      </td>
 +
      <td valign="top" class="td26">
 +
        <p class="p3"><span class="s1">5.0E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td27">
 +
        <p class="p3"><span class="s1"><b>1.0E-02</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td28">
 +
        <p class="p3"><span class="s1">1.6E-06</span></p>
 +
      </td>
 +
      <td valign="top" class="td29">
 +
        <p class="p3"><span class="s1">1.6E-02</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td20">
 +
        <p class="p2"><span class="s1"><b>(30°C, 20mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td21">
 +
        <p class="p3"><span class="s1">6.4E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td22">
 +
        <p class="p3"><span class="s1">1.0E-04</span></p>
 +
      </td>
 +
      <td valign="top" class="td23">
 +
        <p class="p3"><span class="s1">2.0E-02</span></p>
 +
      </td>
 +
      <td valign="top" class="td24">
 +
        <p class="p3"><span class="s1">1.6E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td25">
 +
        <p class="p3"><span class="s1">3.9E-09</span></p>
 +
      </td>
 +
      <td valign="top" class="td26">
 +
        <p class="p3"><span class="s1">1.0E-04</span></p>
 +
      </td>
 +
      <td valign="top" class="td27">
 +
        <p class="p3"><span class="s1"><b>2.0E-02</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td28">
 +
        <p class="p3"><span class="s1">7.9E-07</span></p>
 +
      </td>
 +
      <td valign="top" class="td29">
 +
        <p class="p3"><span class="s1">3.9E-03</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td10">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td30">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td12">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td13">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td14">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td15">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td16">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td30">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td18">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
      <td valign="top" class="td19">
 +
        <p class="p1"><br></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td20">
 +
        <p class="p2"><span class="s1"><b>(37°C, 5mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td21">
 +
        <p class="p3"><span class="s1">1.6E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td22">
 +
        <p class="p3"><span class="s1">2.5E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td23">
 +
        <p class="p3"><span class="s1">5.0E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td24">
 +
        <p class="p3"><span class="s1">6.2E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td25">
 +
        <p class="p3"><span class="s1">1.5E-08</span></p>
 +
      </td>
 +
      <td valign="top" class="td26">
 +
        <p class="p3"><span class="s1">2.5E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td27">
 +
        <p class="p3"><span class="s1"><b>5.0E-03</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td28">
 +
        <p class="p3"><span class="s1">3.1E-06</span></p>
 +
      </td>
 +
      <td valign="top" class="td29">
 +
        <p class="p3"><span class="s1">6.2E-02</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td20">
 +
        <p class="p2"><span class="s1"><b>(37°C, 10mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td21">
 +
        <p class="p3"><span class="s1">3.2E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td22">
 +
        <p class="p3"><span class="s1">5.0E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td23">
 +
        <p class="p3"><span class="s1">1.0E-02</span></p>
 +
      </td>
 +
      <td valign="top" class="td24">
 +
        <p class="p3"><span class="s1">3.1E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td25">
 +
        <p class="p3"><span class="s1">7.7E-09</span></p>
 +
      </td>
 +
      <td valign="top" class="td26">
 +
        <p class="p3"><span class="s1">5.0E-05</span></p>
 +
      </td>
 +
      <td valign="top" class="td27">
 +
        <p class="p3"><span class="s1"><b>1.0E-02</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td28">
 +
        <p class="p3"><span class="s1">1.5E-06</span></p>
 +
      </td>
 +
      <td valign="top" class="td29">
 +
        <p class="p3"><span class="s1">1.5E-02</span></p>
 +
      </td>
 +
    </tr>
 +
    <tr>
 +
      <td valign="top" class="td10">
 +
        <p class="p2"><span class="s1"><b>(37°C, 20mM)</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td11">
 +
        <p class="p3"><span class="s1">6.4E-03</span></p>
 +
      </td>
 +
      <td valign="top" class="td12">
 +
        <p class="p3"><span class="s1">1.0E-04</span></p>
 +
      </td>
 +
      <td valign="top" class="td13">
 +
        <p class="p3"><span class="s1">2.0E-02</span></p>
 +
      </td>
 +
      <td valign="top" class="td14">
 +
        <p class="p3"><span class="s1">1.6E-01</span></p>
 +
      </td>
 +
      <td valign="top" class="td15">
 +
        <p class="p3"><span class="s1">3.8E-09</span></p>
 +
      </td>
 +
      <td valign="top" class="td16">
 +
        <p class="p3"><span class="s1">1.0E-04</span></p>
 +
      </td>
 +
      <td valign="top" class="td17">
 +
        <p class="p3"><span class="s1"><b>2.0E-02</b></span></p>
 +
      </td>
 +
      <td valign="top" class="td18">
 +
        <p class="p3"><span class="s1">7.7E-07</span></p>
 +
      </td>
 +
      <td valign="top" class="td19">
 +
        <p class="p3"><span class="s1">3.9E-03</span></p>
 +
      </td>
 +
    </tr>
 +
  </tbody>
 +
</table>
 +
<p class="p1"><br></p>

Revision as of 11:39, 17 July 2014

Lab Book

Information will be posted here soon! - Watch this space

Modelling

Model of part B possible repression and activation network scenarios

Finished the first draft of the model, will leave it until we have real data to feed back into the system. The model is very robust and allows any user to input a large variety of parameters and scenarios that could be realistically expected in the laboratory results. The output of the model is the colour that you can expect over time (the outputs of the real system will be from a combination of mCherry and GFP).

The model reveals surprising results, including how even a small basal rate of gene expression (due to leakage of the promoters) can really change the results.

Information on how to use Matlab to model repressor and activator networks very easily, accurately and quickly will be uploaded to this wiki soon! If you want more details please don't hesitate to contact us.


An example of the model's output


[DCM] calibration for solution-vapour equilibration

Testing the tolerance of E-coli and Pseudomonas strains to various concentrations of DCM (0mM, 5mM, 10mM, 20mM), the 15 mL falcon tube-contained system is modeled as a real binary solution/ideal gas, based on literature solubility data1, confirming negligible [DCM] deviation:

<img src="http://latex.codecogs.com/gif.latex?p_{i}=c*k^{\Theta&space;}e^{\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}(\frac{1}{T}-\frac{1}{298.15K})}" title="p_{i}=c*k^{\Theta }e^{\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}(\frac{1}{T}-\frac{1}{298.15K})}" />


<img src="http://latex.codecogs.com/gif.latex?k^\Theta=3.9*10^{-6}&space;\:&space;mol&space;\:&space;kg^{-1}&space;Pa^{-1},&space;\frac{\mathrm{d}&space;lnk}{\mathrm{d}&space;1/T}=&space;3900&space;\:K" title="k^\Theta=3.9*10^{-6} \: mol \: kg^{-1} Pa^{-1}, \frac{\mathrm{d} lnk}{\mathrm{d} 1/T}= 3900 \:K" />


<tbody> </tbody>


V(DCM) added (± 5E-4) /ml

n(DCM)(l) unadjusted (± 8E-6) /mol

[DCM] unadjusted (± 2E-3) /M

p(DCM)

(± 4E-2) /kPa

n(DCM)(g)

(± 4E-7) /mol

n(DCM)(l) (± 9E-6) adjusted /mol

[DCM] adjusted

(± 2E-3) /M

Δ[DCM] /M

[DCM] % deviation

(30°C, 5mM)

1.6E-03

2.5E-05

5.0E-03

6.2E-01

1.6E-08

2.5E-05

5.0E-03

3.1E-06

6.3E-02

(30°C, 10mM)

3.2E-03

5.0E-05

1.0E-02

3.1E-01

7.9E-09

5.0E-05

1.0E-02

1.6E-06

1.6E-02

(30°C, 20mM)

6.4E-03

1.0E-04

2.0E-02

1.6E-01

3.9E-09

1.0E-04

2.0E-02

7.9E-07

3.9E-03











(37°C, 5mM)

1.6E-03

2.5E-05

5.0E-03

6.2E-01

1.5E-08

2.5E-05

5.0E-03

3.1E-06

6.2E-02

(37°C, 10mM)

3.2E-03

5.0E-05

1.0E-02

3.1E-01

7.7E-09

5.0E-05

1.0E-02

1.5E-06

1.5E-02

(37°C, 20mM)

6.4E-03

1.0E-04

2.0E-02

1.6E-01

3.8E-09

1.0E-04

2.0E-02

7.7E-07

3.9E-03



</div>

Retrieved from "http://2014.igem.org/Team:Oxford/notebook"