Difference between revisions of "IGEM:IMPERIAL/2008/Prototype/Drylab"

From OpenWetWare
Jump to: navigation, search
m
m (Motility Data Collection & Analysis)
Line 12: Line 12:
 
To build the ODE model, each [[IGEM:IMPERIAL/2008/Prototype/Wetlab/test_constructs | test construct]] was [[/ODE_models_of_test_constructs | individually modelled]]. These test construct models can then be combined and the combined models compared to the experimental results from the wetlab.
 
To build the ODE model, each [[IGEM:IMPERIAL/2008/Prototype/Wetlab/test_constructs | test construct]] was [[/ODE_models_of_test_constructs | individually modelled]]. These test construct models can then be combined and the combined models compared to the experimental results from the wetlab.
  
= [[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection | Motility Data Collection & Analysis ]]=
+
= [[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection | Motility Data Acquisition & Analysis ]]=
  
 
Using a video microscope, we have captured numerous frames of Bacillus Subtilis swimming. Using a manual tracking plug-in for ImageJ, we intend to acquire as much data as possible on the swimming motility of the cells.  
 
Using a video microscope, we have captured numerous frames of Bacillus Subtilis swimming. Using a manual tracking plug-in for ImageJ, we intend to acquire as much data as possible on the swimming motility of the cells.  

Revision as of 15:40, 3 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 {

   border:2px;
   margin:0;
   padding:0pt 1.5pt;
   font-size:8pt;
   text-align:right;
   background-color:#FFFFFF;
   }
  1. bodyContent table.month a { background:none; padding:0 }

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

<html><a href=http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype><img width=50px src=http://openwetware.org/images/f/f2/Imperial_2008_Logo.png></img</a></html> Home The Project B.subtilis Chassis Wet Lab Dry Lab Notebook

<html> <style type="text/css"> div.Section { font:11pt/16pt Calibri, Verdana, Arial, Geneva, sans-serif; }

/* 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; }

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

/* Subsubheadings */ div.Section h3 { font:16pt Calibri, Verdana, Arial, sans-serif; font-weight:bold; color:#3366FF; margin-left:10px; }

/* Subsubsubheadings */ div.Section h4 { font:12pt Calibri, Verdana, Arial, sans-serif; color:#3366FF; margin-left:15px; }

/* 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; }

  1. sddm {

margin: 0; padding: 0; z-index: 30 }

  1. sddm li {

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

  1. sddm li a {

display: block; margin: 0px 0px 0px 0px; padding: 0 0 12px 0; background: #33bbff; color: #FFFFFF; text-align: center; text-decoration: none; }

  1. sddm li a:hover {

border: 0px }

  1. sddm div {

position: absolute; visibility: hidden; margin: 0; padding: 0; background: #33bbff; border: 1px solid #33bbff } #sddm div a { position: relative; 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: #33bbff; color: #FFFFFF } </style></html>


Team Strategy

We have divided the modelling team into 3 sections:

  1. Modelling Genetic Circuits - Erika
  2. Collecting Motility Data - Yanis
  3. Analysis of Motlity Data and Model Fitting - Clinton & Prudence

Modelling the Genetic Circuit

A simple ODE model was assumed in order to model the concentrations of the interacting proteins.

To build the ODE model, each test construct was individually modelled. These test construct models can then be combined and the combined models compared to the experimental results from the wetlab.

Motility Data Acquisition & Analysis

Using a video microscope, we have captured numerous frames of Bacillus Subtilis swimming. Using a manual tracking plug-in for ImageJ, we intend to acquire as much data as possible on the swimming motility of the cells.


Validating the Tracking Software

For our motility analysis we will be using ImageJ (open source freeware software written by NIH). We have considered a few tracking plugins for ImageJ. The most accurate seems to be SpotTracker written by EPFL ( Ecole Polytechnique Federale de Lausanne), though not written specifically for cell tracking. Thus the need for us to validate the software and delimit its range of operability.

Modelling the Growth of B.Subtilis

Modelling the swimming motility

Data Analysis

Resources

The following are four tutorials which introduce us to data analysis and modelling. The tutorials are focused on the above approach. MATLAB codes used for data analysis can be found in the final link.

Dry Lab Tutorial 1: Design of a Motility Assay

Dry Lab Tutorial 2: Statistical Data Analysis

Dry Lab Tutorial 3: Testing the Tracking Software

Dry Lab Tutorial 4: Modelling the Growth Curve

MATLAB Codes

References


<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>

</td></tr></table>