Team:DTU-Denmark/Achievements/Calculator

From 2014.igem.org

(Difference between revisions)

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

@@ Line 2: / Line 2: @@
 <html>
+<script>
+$(document).ready(function() {
+    $("#calc-input").trigger("input");
+});
+</script>
 <style>
 #PoPScalculator table td {
@@ Line 32: / Line 37: @@
 <div id="PoPScalculator" style="width:800px;position:relative;">
-<form onchange = "
+<form id = "calc-input" onchange = "
-var conc = parseFloat(concentration.value);
+conc = (parseFloat(fluorescence.value)-parseFloat(intercept.value)) / parseFloat(slope.value);
-var CFUcount = parseFloat(CFU.value);
+CFUcount = parseFloat(CFU.value);
-var fold = parseFloat(foldfraction.value);
+fold = parseFloat(foldfraction.value);
+degenvar = parseFloat(degen.value)/parseFloat(degenunit.value);
-if (degcheck.checked) { degen.value = Math.log(2)/(parseFloat(deghalf.value)*parseFloat(deghalfunit.value)) };
+growthvar = parseFloat(growth.value)/parseFloat(growthunit.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) { 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(conc)/(parseFloat(CFUcount)/1000000000000)*(602200/(parseFloat(fold)/100)))*((parseFloat(degen.value)/parseFloat(degenunit.value))+(parseFloat(growth.value)/parseFloat(growthunit.value)))/parseFloat(copynumber.value);
-activity.value = Math.round(parseFloat(activity.value)*100000)/100000;
-activity.value = parseFloat(activity.value).toExponential();
 ">
 <table>
-    <tr height="169">
+    <tr style="height:169px;">
-       <td width="394">
+       <td style="width:394px;">
 <table height="80" width="360">
    <tr>
-     <td width="63%" colspan="2">
+     <td width="71%" colspan="2">
      Fluorescence:
      </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 width="21%"></td>
+     <td width="15%"></td>
    </tr>
    <tr>
@@ Line 68: / Line 89: @@
      </td>
      <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 width="21%"></td>
+     <td width="15%"></td>
    </tr>
@@ Line 78: / Line 99: @@
      </td>
      <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 width="21%"></td>
+     <td width="15%"></td>
    </tr>
@@ Line 88: / Line 109: @@
      </td>
      <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>
    </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>
 </table>
      </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>
@@ Line 102: / Line 142: @@
 <table height="80px" width="360">
    <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;">
          <input name="CFU" type="number" step="any" min="0" style="width:90px"/>
@@ Line 109: / Line 149: @@
    </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>
    </tr>
@@ Line 119: / Line 159: @@
      <td width="63%">OD600</td>
      <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 width="21%">
@@ Line 133: / Line 173: @@
      <td width="63%" colspan="2">Degradation rate:</td>
      <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 width="21%" style="padding-top:4px">
+     <td width="21%" style="padding-top:3px">
 	<select name="degenunit" style="width:80px">
 	<option value="3600">per hour</option>
@@ Line 144: / Line 184: @@
    </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>
 </table>
@@ Line 153: / Line 193: @@
      <td width="63%">Degradation half time:</td>
      <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 width="21%" style="padding-top:4px">
 	<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>
 	</td>
@@ Line 172: / Line 212: @@
      <td width="63%" colspan="2">Growth rate:</td>
      <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:4px">
+     <td width="21%" style="padding-top:3px">
 	<select name="growthunit" style="width:80px">
 	<option value="3600">per hour</option>
@@ Line 182: / Line 222: @@
    </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>
 </table>
@@ Line 191: / Line 231: @@
      <td width="63%">Growth doubling time:</td>
      <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">
 	<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>
 	</td>
@@ Line 208: / Line 248: @@
      <td width="63%">Fold-fraction:</td>
      <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 width="21%">%</td>
@@ Line 215: / Line 255: @@
      <td width="63%">Copy number:</td>
      <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="21%">
+     </td>
      <td width="21%"></td>
    </tr>
 </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 height=231>
      <td>
-<table>
+<table style="padding-top:70px;">
    <tr>
-     <td width="63%">Promoter activity</td>
+     <td colspan="2"><center>Promoter activity</center></td>
-     <td width="16%" style="text-align:right"><output name="activity" type="number" step="0.1"></output></td>
+  </tr>
-     <td width="21%">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>
 </table>
@@ Line 236: / Line 289: @@
 </div>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>