Team:DTU-Denmark/Achievements/Calculator

From 2014.igem.org

(Difference between revisions)
 
(200 intermediate revisions not shown)
Line 2: Line 2:
<html>
<html>
 +
<script>
 +
$(document).ready(function() {
 +
    $("#calc-input").trigger("input");
 +
});
 +
</script>
<style>
<style>
#PoPScalculator table td {
#PoPScalculator table td {
Line 32: Line 37:
<div id="PoPScalculator" style="width:800px;position:relative;">
<div id="PoPScalculator" style="width:800px;position:relative;">
 +
<form id = "calc-input" onchange = "
-
<form oninput = "
 
-
if (degcheck.checked) { degen.value = Math.log(2)/(parseFloat(deghalf.value)*parseFloat(deghalfunit.value)) };
 
-
if (growthcheck.checked) { growth.value = Math.log(2)/(parseFloat(grodouble.value)*parseFloat(grodoubleunit.value)) };
 
-
if (CFUcheck.checked) { CFU.value = (parseFloat(OD600.value)/1000000000000) };
 
-
if (conccheck.checked) { concentration.value = { (parseFloat(fluorescence.value) - parseFloat(intercept.value)) / parseFloat(slope.value) ;
 
-
activity.value = (parseFloat(concentration.value)/(parseFloat(CFU.value)*10000000000000)*(602200/(parseFloat(foldfraction.value)/100)))*((parseFloat(degen.value)/parseFloat(degenunit.value))+(parseFloat(growth.value)/parseFloat(growthunit.value)))/parseFloat(copynumber.value);
 
-
num = parseFloat(activity.value);
+
conc = (parseFloat(fluorescence.value)-parseFloat(intercept.value)) / parseFloat(slope.value);
 +
CFUcount = parseFloat(CFU.value);
 +
fold = parseFloat(foldfraction.value);
 +
degenvar = parseFloat(degen.value)/parseFloat(degenunit.value);
-
num = Math.round(parseFloat(num) * 10000000 ) / 10000000 ;
+
growthvar = parseFloat(growth.value)/parseFloat(growthunit.value);
 +
 
 +
 
 +
 
 +
if (conccheck.checked) { conc = parseFloat(concentration.value) };
 +
if (degcheck.checked) { degenvar = Math.log(2)/(parseFloat(deghalf.value)*parseFloat(deghalfunit.value)) };
 +
if (growthcheck.checked) { growthvar = Math.log(2)/(parseFloat(grodouble.value)*parseFloat(grodoubleunit.value)) };
 +
if (CFUcheck.checked) { CFUcount = (parseFloat(OD600.value)*1e12) };
 +
 
 +
 
 +
 
 +
activity1 = (parseFloat(conc)/(parseFloat(CFUcount)/1e12)*(602200/(parseFloat(fold)/100)))*((parseFloat(degenvar))+(parseFloat(growthvar)))/parseFloat(copynumber.value);
 +
 
 +
 
 +
if (activity1 <= 0.01 || activity1 >= 100) {
 +
  activity.value = activity1.toExponential(2);
 +
} else {
 +
activity.value = (Math.round(activity1*1000))/1000;
 +
}
 +
 
 +
activity2.value = activity.value;
-
activity.value = parseFloat(num);
 
Line 50: 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="55%" colspan="2">
+
     <td width="71%" colspan="2">
     Fluorescence:
     Fluorescence:
     </td>
     </td>
-
     <td width="23%" 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="22%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
   <tr>
   <tr>
Line 67: 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="22%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
Line 77: 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="22%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
Line 87: 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="22%"></td>
+
     <td width="15%"></td>
   </tr>
   </tr>
</table>
</table>
     </td>
     </td>
 +
    <td style="font-size:10px; line-height:130%; padding: 10px 20px 10px 10px;">
 +
 +
<p style="font-size:12px; font-weight:150%;">&#160;&#160;&#160;PoPS calculator V. 1.0</p>
 +
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 <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.
 +
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>.
 +
 +
 +
    </td>
 +
 +
 +
 +
   </tr>
   </tr>
   <tr>
   <tr>
Line 101: Line 142:
<table height="80px" width="360">
<table height="80px" width="360">
   <tr>
   <tr>
-
     <td width="55%" colspan="2">CFU count</td>
+
     <td width="63%" colspan="2">Cell density:</td>
-
     <td width="23%" 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"/>
     </td>
     </td>
-
     <td width="22%">CFU/L</td>
+
     <td width="21%">CFU/L</td>
   </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="22%"></td>
+
     <td width="21%"></td>
   </tr>
   </tr>
</table>
</table>
Line 116: Line 157:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%">OD600</td>
+
     <td width="63%">OD600</td>
-
     <td width="23%" 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="22%">
+
     <td width="21%">
     </td>
     </td>
   </tr>
   </tr>
Line 130: Line 171:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%" colspan="2">Degradation rate:</td>
+
     <td width="63%" colspan="2">Degradation rate:</td>
-
     <td width="23%" 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="22%" style="padding-top:4px">
+
     <td width="21%" style="padding-top:3px">
<select name="degenunit" style="width:80px">
<select name="degenunit" style="width:80px">
<option value="3600">per hour</option>
<option value="3600">per hour</option>
Line 143: 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 150: Line 191:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%">Degradation half time:</td>
+
     <td width="63%">Degradation half time:</td>
-
     <td width="23%" 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="22%" style="padding-top:4px">
+
     <td width="21%" style="padding-top:4px">
<select name="deghalfunit">
<select name="deghalfunit">
-
<option value="3600">h</option>
+
<option value="3600">hours</option>
-
<option value="60">m</option>
+
<option value="60">minutes</option>
-
<option value="1">s</option>
+
<option value="1">seconds</option>
</select>
</select>
</td>
</td>
Line 169: Line 210:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%" colspan="2">Growth rate:</td>
+
     <td width="63%" colspan="2">Growth rate:</td>
-
     <td width="23%" 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="22%" style="padding-top:4px">
+
     <td width="21%" style="padding-top:3px">
<select name="growthunit" style="width:80px">
<select name="growthunit" style="width:80px">
<option value="3600">per hour</option>
<option value="3600">per hour</option>
Line 181: 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 188: Line 229:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%">Growth doubling time:</td>
+
     <td width="63%">Growth doubling time:</td>
-
     <td width="23%" 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="22%" style="padding-top:4px">
+
     <td width="21%" style="padding-top:4px">
<select name="grodoubleunit">
<select name="grodoubleunit">
-
<option value="3600">h</option>
+
<option value="3600">hours</option>
-
<option value="60">m</option>
+
<option value="60">minutes</option>
-
<option value="1">s</option>
+
<option value="1">seconds</option>
</select>
</select>
</td>
</td>
Line 205: Line 246:
<table width="360">
<table width="360">
   <tr>
   <tr>
-
     <td width="55%">Fold-fraction:</td>
+
     <td width="63%">Fold-fraction:</td>
-
     <td width="23%" 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="22%">%</td>
+
     <td width="21%">%</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <td width="55%">Copy number:</td>
+
     <td width="63%">Copy number:</td>
-
     <td width="23%" 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 width="22%">
+
     </td>
-
     <td width="22%"></td>
+
     <td width="21%"></td>
   </tr>
   </tr>
</table>
</table>
 +
    <td rowspan="2" style="padding: 30px 50px 50px 163px;">
 +
<table>
 +
  <tr>
 +
    <td width="37%">
 +
    <output name="activity2" type="number" step="0.1"></output>
 +
    </td>
 +
    <td width="50%">PoPS
 +
    </td>
 +
  </tr>
 +
</table>
 +
    </td>
   </tr>
   </tr>
   <tr height=231>
   <tr height=231>
     <td>
     <td>
-
<table>
+
<table style="padding-top:70px;">
   <tr>
   <tr>
-
     <td width="55%">Promoter activity</td>
+
     <td colspan="2"><center>Promoter activity</center></td>
-
     <td width="23%" style="text-align:right"><output name="activity" type="number" step="0.1"></output></td>
+
  </tr>
-
     <td width="22%">PoPS</td>
+
  <tr>
 +
     <td width="50%" style="text-align:right"><output name="activity" type="number" step="0.1"></output></td>
 +
     <td width="50%">&#160;PoPS</td>
   </tr>
   </tr>
</table>
</table>
Line 235: Line 289:
</div>
</div>
-
 
-
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
<br>
 
-
 
-
<br>
 

Latest revision as of 02:38, 18 October 2014

Technical University of Denmark

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
Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
+45 45 25 25 25
dtuigem14@gmail.com .

Retrieved from "http://2014.igem.org/Team:DTU-Denmark/Achievements/Calculator"