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== [[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation | Validating the Tracking Software ]] ==  
= [[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation | 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 '''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation | validate ]]''' the software and delimit its range of operability.
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 '''[[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation | validate ]]''' the software and delimit its range of operability.

Revision as of 15:43, 3 September 2008

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<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

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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


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