Team:DTU-Denmark/Achievements/Calculator

From 2014.igem.org

(Difference between revisions)
 
(43 intermediate revisions not shown)
Line 59: Line 59:
-
activity.value = activity1.toExponential(2) ;
+
if (activity1 <= 0.01 || activity1 >= 100) {
 +
  activity.value = activity1.toExponential(2);
 +
} else {
 +
activity.value = (Math.round(activity1*1000))/1000;
 +
}
-
activity2.value = activity1.toExponential(2) ;
+
activity2.value = activity.value;
Line 68: Line 72:
<table>
<table>
-
   <tr height="169">
+
   <tr style="height:169px;">
-
       <td width="394">
+
       <td style="width:394px;">
<table height="80" width="360">
<table height="80" width="360">
   <tr>
   <tr>
-
     <td width="63%" colspan="2">
+
     <td width="71%" colspan="2">
     Fluorescence:
     Fluorescence:
     </td>
     </td>
-
     <td width="16%" style="text-align:right; padding-top: 3px;">
+
     <td width="14%" style="text-align:right; padding-top: 3px;">
-
     <input name="fluorescence" type="number" step="any" min="0" placeholder="value" style="width:90px" />
+
     <input name="fluorescence" type="number" step="any" min="0" style="width:90px" />
     </td>
     </td>
-
     <td width="21%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
   <tr>
   <tr>
Line 85: Line 89:
     </td>
     </td>
     <td style="text-align:right; padding-top: 3px;">
     <td style="text-align:right; padding-top: 3px;">
-
     <input name="slope" type="number" step="any" min="0" placeholder="slope" style="width:90px" />
+
     <input name="slope" type="number" step="any" min="0" style="width:90px" />
     </td>
     </td>
-
     <td width="21%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
Line 95: Line 99:
     </td>
     </td>
     <td style="text-align:right; padding-top: 3px;">
     <td style="text-align:right; padding-top: 3px;">
-
     <input name="intercept" type="number" step="any" min="0" placeholder="intercept" style="width:90px" />
+
     <input name="intercept" type="number" step="any" min="0" style="width:90px" />
     </td>
     </td>
-
     <td width="21%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
Line 105: Line 109:
     </td>
     </td>
     <td style="text-align:right; padding-top: 3px;">
     <td style="text-align:right; padding-top: 3px;">
-
     <input name="concentration" type="number" step="any" min="0" placeholder="Enter number" value="0.45" style="width:90px" />
+
     <input name="concentration" type="number" step="any" min="0" style="width:90px" />
     <td>µM</td>
     <td>µM</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="conccheck"></td><td colspan="2" width="71%">Input concentration directly</td>
+
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="conccheck"></td><td colspan="2" width="71%">Calculate from concentration</td>
-
     <td width="21%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
</table>
</table>
Line 122: Line 126:
Fluorescence per spinach (slope of a standard series).
Fluorescence per spinach (slope of a standard series).
Background fluorescence from your culture (intercept).
Background fluorescence from your culture (intercept).
-
CFU/L or optical density at 600 nm (OD600) for your measured culture.
+
CFU/L or optical density at 600 nm (OD600) for your examined culture.
We have found degradation rate of Spinach in <i>E. coli</i> when grown in LB at 37 &deg;C  so feel free to use this value.
We have found degradation rate of Spinach in <i>E. coli</i> when grown in LB at 37 &deg;C  so feel free to use this value.
You also need a growth rate for your culture, and the copy number of the Spinach sequence per cell.
You also need a growth rate for your culture, and the copy number of the Spinach sequence per cell.
-
When your values are entered to the calculator you will receive your result, the calculator works using the formula derived <a href"https://2014.igem.org/Team:DTU-Denmark/Achievements/Modelling">here</a>
+
When your values are entered to the calculator you will receive your result, the calculator works using the formula derived <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/Modelling">here</a>.
Line 138: Line 142:
<table height="80px" width="360">
<table height="80px" width="360">
   <tr>
   <tr>
-
     <td width="63%" colspan="2">CFU count</td>
+
     <td width="63%" colspan="2">Cell density:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
         <input name="CFU" type="number" step="any" min="0" style="width:90px"/>
         <input name="CFU" type="number" step="any" min="0" style="width:90px"/>
Line 145: Line 149:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="CFUcheck"></td><td colspan="2" width="71%">Use OD measurement</td>
+
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="CFUcheck"></td><td colspan="2" width="71%">Calculate from OD measurement</td>
     <td width="21%"></td>
     <td width="21%"></td>
   </tr>
   </tr>
Line 155: Line 159:
     <td width="63%">OD600</td>
     <td width="63%">OD600</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="OD600" type="number" step="any" min="0" placeholder="Enter number" value="6.3" style="width:90px" />
+
         <input name="OD600" type="number" step="any" min="0" style="width:90px" />
     </td>
     </td>
     <td width="21%">
     <td width="21%">
Line 169: Line 173:
     <td width="63%" colspan="2">Degradation rate:</td>
     <td width="63%" colspan="2">Degradation rate:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
     <input name="degen" type="number" step="any" min="0" placeholder="rate" value="0.083" style="width:90px" />
+
     <input name="degen" type="number" step="any" min="0" placeholder="0.740" value="0.740" style="width:90px" />
     </td>
     </td>
     <td width="21%" style="padding-top:3px">
     <td width="21%" style="padding-top:3px">
Line 180: Line 184:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="degcheck"></td><td colspan="2" width="74%">Use degradation half time</td>
+
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="degcheck"></td><td colspan="2" width="74%">Calculate from half time</td>
   </tr>
   </tr>
</table>
</table>
Line 189: Line 193:
     <td width="63%">Degradation half time:</td>
     <td width="63%">Degradation half time:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="deghalf" type="number" step="any" min="0" placeholder="Half time" style="width:90px" />
+
         <input name="deghalf" type="number" step="any" min="0" placeholder="0.937" value="0.937" style="width:90px" />
</td>
</td>
     <td width="21%" style="padding-top:4px">
     <td width="21%" style="padding-top:4px">
Line 208: Line 212:
     <td width="63%" colspan="2">Growth rate:</td>
     <td width="63%" colspan="2">Growth rate:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="growth" type="number" step="any" min="0" placeholder="growth" value="0.83" style="width:90px" />
+
         <input name="growth" type="number" step="any" min="0" placeholder="0.797" value="0.797" style="width:90px" />
     <td width="21%" style="padding-top:3px">
     <td width="21%" style="padding-top:3px">
<select name="growthunit" style="width:80px">
<select name="growthunit" style="width:80px">
Line 218: Line 222:
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="growthcheck"></td><td colspan="2" width="74%">Use growth doubling time<br></td>
+
     <td width="7%" style="padding-top:7px"><input type="checkbox" name="growthcheck"></td><td colspan="2" width="74%">Calculate from doubling time<br></td>
   </tr>
   </tr>
</table>
</table>
Line 227: Line 231:
     <td width="63%">Growth doubling time:</td>
     <td width="63%">Growth doubling time:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="grodouble" type="number" step="any" min="0" placeholder="Doubling time" style="width:90px" />
+
         <input name="grodouble" type="number" step="any" min="0" placeholder="0.870" value="0.870" style="width:90px" />
     <td width="21%" style="padding-top:4px">
     <td width="21%" style="padding-top:4px">
<select name="grodoubleunit">
<select name="grodoubleunit">
Line 244: Line 248:
     <td width="63%">Fold-fraction:</td>
     <td width="63%">Fold-fraction:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="foldfraction" type="number" step="any" min="0" placeholder="Enter number" value="50" style="width:90px" />
+
         <input name="foldfraction" type="number" step="any" min="0" placeholder="60" value="60" style="width:90px" />
</td>
</td>
     <td width="21%">%</td>
     <td width="21%">%</td>
Line 251: Line 255:
     <td width="63%">Copy number:</td>
     <td width="63%">Copy number:</td>
     <td width="16%" style="text-align:right; padding-top: 3px;">
     <td width="16%" style="text-align:right; padding-top: 3px;">
-
         <input name="copynumber" type="number" step="any" min="0" placeholder="Enter number" value="300" style="width:90px" />
+
         <input name="copynumber" type="number" step="any" min="0" style="width:90px" />
     </td>
     </td>
     <td width="21%"></td>
     <td width="21%"></td>
Line 257: Line 261:
</table>
</table>
     <td rowspan="2" style="padding: 30px 50px 50px 163px;">
     <td rowspan="2" style="padding: 30px 50px 50px 163px;">
-
<table width="40%">
+
<table>
   <tr>
   <tr>
-
     <td width="30%">
+
     <td width="37%">
     <output name="activity2" type="number" step="0.1"></output>
     <output name="activity2" type="number" step="0.1"></output>
     </td>
     </td>
-
     <td width="50">PoPS
+
     <td width="50%">PoPS
     </td>
     </td>
   </tr>
   </tr>
Line 285: Line 289:
</div>
</div>
-
 
-
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
<br>
 

Latest revision as of 02:38, 18 October 2014

Fluorescence:
Standard curve, intercept:
Standard curve, slope:
Spinach concentration: µM
Calculate from concentration

   PoPS calculator V. 1.0

This calculator allows you to calculate your promoter activity in PoPS (Polymerases Per Second) In order to use it you need to obtain: Fluorescence signal from your culture. Fluorescence per spinach (slope of a standard series). Background fluorescence from your culture (intercept). CFU/L or optical density at 600 nm (OD600) for your examined culture. We have found degradation rate of Spinach in E. coli when grown in LB at 37 °C so feel free to use this value. You also need a growth rate for your culture, and the copy number of the Spinach sequence per cell. When your values are entered to the calculator you will receive your result, the calculator works using the formula derived here.
Cell density: CFU/L
Calculate from OD measurement
OD600
Degradation rate:
Calculate from half time
Degradation half time:
Growth rate:
Calculate from doubling time
Growth doubling time:
Fold-fraction: %
Copy number:
PoPS
Promoter activity
 PoPS