IGEM:IMPERIAL/2008/Prototype/Drylab: Difference between revisions
mNo edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
We have divided the modelling team into 3 sections: | We have divided the modelling team into 3 sections: | ||
#Modelling Genetic Circuits - Erika | #Modelling Genetic Circuits - Erika | ||
#Collecting Motility Data - Yanis | #Modelling ''B.Subtilis'' Growth - Prudence | ||
#Modelling ''B.Subtilis'' Motility | |||
**Collecting Motility Data - Yanis | |||
**Analysis of Motlity Data and Model Fitting - Clinton | |||
=[[/ODE_Model | Modelling the Genetic Circuit]]= | =[[/ODE_Model | Modelling the Genetic Circuit]]= | ||
Revision as of 05:43, 6 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; }
- 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; }
- sddm {
margin: 0; padding: 0; z-index: 30 }
- sddm li {
margin: 0; padding: 0; list-style: none; float: center; font: bold 12pt Calibri, Verdana, Arial, Geneva, sans-serif; border: 0px }
- 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; }
- sddm li a:hover {
border: 0px }
- 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:
- Modelling Genetic Circuits - Erika
- Modelling B.Subtilis Growth - Prudence
- Modelling B.Subtilis Motility
- Collecting Motility Data - Yanis
- Analysis of Motlity Data and Model Fitting - Clinton
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.
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.
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.
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
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>
