Difference between revisions of "IGEM:IMPERIAL/2008/New/Motility"

From OpenWetWare
Jump to: navigation, search
Line 15: Line 15:
Authors: Clinton and Yanis
Editors: Erika
Why model motility - crucial to our project as it has has a motility function
Data gathering - link to wetlab
Synthetic data generation

Revision as of 14:39, 11 September 2008

<html> <style type="text/css"> .firstHeading {display: none;} </style> </html> <html> <style type="text/css">

   table.calendar          { margin:0; padding:2px; }

table.calendar td { margin:0; padding:1px; vertical-align:top; } table.month .heading td { padding:1px; background-color:#FFFFFF; text-align:center; font-size:120%; font-weight:bold; } table.month .dow td { text-align:center; font-size:110%; } table.month td.today { background-color:#3366FF } table.month td {

   padding:0pt 1.5pt;
  1. bodyContent table.month a { background:none; padding:0 }

.day-active { font-weight:bold; } .day-empty { color:black; } </style> </html>

<html><script language="JavaScript">

var timeout = 250; var closetimer = 0; var ddmenuitem = 0;

// open hidden layer function mopen(id) { // cancel close timer mcancelclosetime(); // close old layer if(ddmenuitem) ddmenuitem.style.visibility = 'hidden'; // get new layer and show it ddmenuitem = document.getElementById(id); ddmenuitem.style.visibility = 'visible'; } // close showed layer function mclose() { if(ddmenuitem) ddmenuitem.style.visibility = 'hidden'; } // go close timer function mclosetime() { closetimer = window.setTimeout(mclose, timeout); } // cancel close timer function mcancelclosetime() { if(closetimer) { window.clearTimeout(closetimer); closetimer = null; } } // close layer when click-out //document.onclick = mclose; </script> <table background="http://i59.photobucket.com/albums/g305/Timpski/ToolbarBackground.png" style="color:#ffffff;" link="#ffffff" cellpadding="0" cellspacing="1" border="0" bordercolor="#ffffff" align="center" width="100%"><tr><td colspan="6" class="wetlab"><br><br><br></td></tr> <tr><td align="center" width="10%" valign="bottom"><ul id="sddm"><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Home"> Home </a></ul> </td><td align="center" width="20%" valign="bottom"><ul id="sddm"><a href="#"

       onmouseout="mclosetime()">Biofabricator Subtilis</a>
       <div id="m1" 
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Project">Project Specifications</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Chassis_1">Why B. subtilis?</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Chassis_2">B. subtilis: Benefits vs Challenges</a>

</td><td align="center" width="18%" valign="bottom"><ul id="sddm"><a href="#"

       onmouseout="mclosetime()">Wet Lab</a>
       <div id="m2" 
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Wet_Lab">Wet Lab Hub</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Cloning_Strategy">Cloning Strategy</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Protocols">Experiments & Protocols</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Major_Results">Experimental Results</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/BioBricks">BioBricks & Characterisation</a>

</td><td align="center" width="18%" valign="bottom"><ul id="sddm"><a href="#"

       onmouseout="mclosetime()">Dry Lab</a>
       <div id="m3" 
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Dry_Lab">Dry Lab Hub</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Growth_Curve">Growth Curves</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Genetic_Circuit">Genetic Circuits</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Motility">Motility Analysis</a>
       <a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Appendices">Appendices - Code etc.</a>

</td><td align="center" width="17%" valign="bottom"><ul id="sddm"><a href="http://2008.igem.org/Team:Imperial_College/Notebook"> Notebook </a></ul> </td><td align="center" width="17%" valign="bottom"><ul id="sddm"><a href="http://openwetware.org/wiki/IGEM:IMPERIAL/2008/New/Team"> Our Team </a></ul> </td></tr></table></html>

<html><style type="text/css">

div.Section { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; background-image: url(http://openwetware.org/images/a/a0/Background.PNG); background-size: 100%; background-origin: content; }

/* Text (paragraphs) */ div.Section p { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:justify; margin-top:0px; margin-left:30px; margin-right:30px; }

/* Headings */ div.Section h1 { font:22pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:left; color:#3366FF; font-weight:bold; }

/* Subheadings */ div.Section h2 { font:18pt Calibri, Verdana, Arial, Geneva, sans-serif; color:#3366FF; margin-left:5px; font-weight:bold; }

/* Subsubheadings */ div.Section h3 { font:22pt Calibri, Verdana, Arial, sans-serif; color:#E5EBFF; margin-left:10px; font-weight:bold; }

/* Subsubsubheadings */ div.Section h4 { font:22pt Calibri, Verdana, Arial, sans-serif; color:#2B48B3; margin-left:10px; font-weight:bold; }

/* Subsubsubsubheadings */ div.Section h5 { font:12pt Calibri, Verdana, Arial, sans-serif; color:#3366FF; margin-left:20px; }

/* References */ div.Section h6 { font:12pt Calibri, Verdana, Arial, sans-serif; font-weight:bold; font-style:italic; color:#3366FF; margin-left:25px; }

/* Hyperlinks */ div.Section a { }

div.Section a:hover { }

/* Tables */ div.Section td { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:justify; vertical-align:top; padding:2px 4px 2px 4px; }

/* Lists */ div.Section li { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align:left; margin-top:0px; margin-left:30px; margin-right:0px; }

/* TOC stuff */ table.toc { margin-left:10px; }

table.toc li { font: 11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; text-align: justify; margin-top: 0px; margin-left:2px; margin-right:2px; }

/* [edit] links */ span.editsection { color:#BBBBBB; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; }

span.editsection a { color:#BBBBBB; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; }

span.editsection a:hover { color:#3366FF; font-size:10pt; font-weight:normal; font-style:normal; vertical-align:bottom; }

/* Drop-down Menu */

  1. sddm {

margin: 0; padding: 0; z-index: 30 margin: 0; padding: 0; float: center; font: bold 12pt Calibri, Verdana, Arial, Geneva, sans-serif; border: 0px; list-style: none; }

  1. sddm a {

display: block; margin: 0px 0px 0px 0px; padding: 0 0 12px 0; color: #FFFFFF; text-align: center; text-decoration: none; }

  1. sddm a:hover {

border: 0px }

  1. sddm div {

position: absolute; visibility: hidden; margin: 0; padding: 0; background: #66aadd; border: 1px solid #66aadd } #sddm div a { position: relative; left: 0; display: block; margin: 0; padding: 5px 10px; width: auto; white-space: nowrap; text-align: left; text-decoration: none; background: #FFFFFF; color: #2875DE; font: 11pt Calibri, Verdana, Arial, Geneva, sans-serif } #sddm div a:hover { background: #66aadd; color: #FFFFFF } </style></html>


Approach to Modelling Motility

The motility of B.Subtilis is hypothesised to be affected by various levels of EpsE expression. In order to model motility as a function of EpsE production, we have decided to use video microscopy techniques to analyse the motility of B.Subtilis. We hope to obtain a transfer function model relating EpsE expression to bacterial motility characteristics such as run velocity, run duration, tumbling angle and tumbling duration. This modelling process is shown on the right and has been divided into 3 main sections:

  1. Validation of Tracking Software
    • In order to assess the error associated with tracking algorithms applied to a digitised images sequence, a series of steps were taken to validate the tracking software.
  2. Motility Data Acquisition
    • Data on run velocity, run duration, tumbling angle and tubmling duration were extracted from coordinate data output provided by the tracking software as part of the process of gathering data.
  3. Model Fitting
    • Several alternative models were created for the purpose of model fitting. The motility data obtained is then analysed and fitted to alternative models. Preferences will then be assigned to fitted models using probabilistic methods such as Bayesian Analysis.

<html><center><table style="color:#ffffff;background-color:#66aadd;" cellpadding="3" cellspacing="1" border="0" bordercolor="#ffffff" align="center"> <tr><td><ul id="sddm"></html>[[IGEM:IMPERIAL/2008/New/{{{1}}}|< Previous]]<html></ul> </td><td><ul id="sddm"><a href="#">Back to top</a></ul> </td><td><ul id="sddm"></html>[[IGEM:IMPERIAL/2008/New/{{{2}}}|Next >]]<html></ul> </td></tr></table> </center></html>