IGEM:IMPERIAL/2008/Prototype/Drylab

=Team Strategy= We have divided the modelling team into 3 sections:
 * 1) Modelling Genetic Circuits - Erika
 * 2) Modelling B.Subtilis Growth - Prudence
 * 3) Modelling B.Subtilis Motility
 * 4) *Collecting Motility Data - Yanis
 * 5) *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:


 * 1)  Validation of Tracking Software 
 * 2) *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.
 * 3) Motility Data Acquisition
 * 4) *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.
 * 5) Model Fitting
 * 6) *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.

[[Media:Tutorial_1.pdf | Dry Lab Tutorial 1: Design of a Motility Assay]]

Dry Lab Tutorial 2: Statistical Data Analysis

[[Media:Testing_Tracking_Software.pdf | Dry Lab Tutorial 3: Testing the Tracking Software]]

[[Media:Modelling_Growth_Curve.pdf | Dry Lab Tutorial 4: Modelling the Growth Curve]]

MATLAB Codes

=References=