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 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) };
-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);
+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);
+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;
@@ Line 46: / Line 72: @@
 <table>
-    <tr height="169">
+    <tr style="height:169px;">
-       <td width="394">
+       <td style="width:394px;">
 <table height="80" width="360">
    <tr>
-     <td width="55%" colspan="2">
+     <td width="71%" colspan="2">
      Fluorescence:
      </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 width="22%"></td>
+     <td width="15%"></td>
    </tr>
    <tr>
@@ Line 63: / 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="22%"></td>
+     <td width="15%"></td>
    </tr>
@@ Line 73: / 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="22%"></td>
+     <td width="15%"></td>
    </tr>
@@ Line 83: / 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="22%"></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 97: / Line 142: @@
 <table height="80px" width="360">
    <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"/>
      </td>
-     <td width="22%">CFU/L</td>
+     <td width="21%">CFU/L</td>
    </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>
 </table>
@@ Line 112: / Line 157: @@
 <table width="360">
    <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 width="22%">
+     <td width="21%">
      </td>
    </tr>
@@ Line 126: / Line 171: @@
 <table width="360">
    <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 width="22%" style="padding-top:4px">
+     <td width="21%" style="padding-top:3px">
 	<select name="degenunit" style="width:80px">
 	<option value="3600">per hour</option>
@@ Line 139: / 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 146: / Line 191: @@
 <table width="360">
    <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 width="22%" style="padding-top:4px">
+     <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 165: / Line 210: @@
 <table width="360">
    <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">
 	<option value="3600">per hour</option>
@@ Line 177: / 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 184: / Line 229: @@
 <table width="360">
    <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">
-	<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 201: / Line 246: @@
 <table width="360">
    <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 width="22%">%</td>
+     <td width="21%">%</td>
    </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>
 </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="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>
 </table>
@@ Line 231: / Line 289: @@
 </div>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>