IGEM:IMPERIAL/2008/Prototype/Drylab
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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.  
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+  = [[IGEM:IMPERIAL/2008/Prototype/Drylab/Validation  Validating the Tracking Software ]] =  
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+  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.  
= [[IGEM:IMPERIAL/2008/Prototype/Drylab/Motility_data_collection  Motility Data Acquisition & 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 plugin 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 plugin for ImageJ, we intend to acquire as much data as possible on the swimming motility of the cells.  
  
  
  
  
  
=[[IGEM:IMPERIAL/2008/Prototype/Drylab/Modelling_the_Growth_of_B.Subtilis Modelling the Growth of B.Subtilis]]=  =[[IGEM:IMPERIAL/2008/Prototype/Drylab/Modelling_the_Growth_of_B.Subtilis Modelling the Growth of B.Subtilis]]= 
Revision as of 13:36, 5 September 2008
Home  The Project  B.subtilis Chassis  Wet Lab  Dry Lab  Notebook 

Contents 
Team Strategy
We have divided the modelling team into 3 sections:
 Modelling Genetic Circuits  Erika
 Collecting Motility Data  Yanis
 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.
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 plugin 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

