IGEM:IMPERIAL/2008/Prototype/Drylab: Difference between revisions
(17 intermediate revisions by the same user not shown) | |||
Line 6: | Line 6: | ||
#Modelling ''B.Subtilis'' Growth - Prudence | #Modelling ''B.Subtilis'' Growth - Prudence | ||
#Modelling ''B.Subtilis'' Motility | #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]]= | ||
Line 14: | Line 14: | ||
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/ | =[[IGEM:IMPERIAL/2008/Prototype/Drylab/Modelling_the_Growth_of_B.Subtilis| Modelling the Growth of ''B.Subtilis'']]= | ||
=Modelling the Motility of ''B.Subtilis''= | |||
[[Image:Approach.jpg|300px|thumb|right|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: | |||
#'''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation | 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 '''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation |validate]]''' the tracking software. | |||
#'''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection|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. | |||
#'''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Data_Analysis|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. | |||
=Resources= | =Resources= |
Latest revision as of 10:07, 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.
Modelling the Growth of B.Subtilis
Modelling the Motility of B.Subtilis
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:
- 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.
- 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.
- 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.
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>