IGEM:IMPERIAL/2008/Prototype/Drylab/Data Analysis/Gather Data
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Gathering Data
Synthetic Data
Synthetic data was first generated for the purpose of model fitting while running microscopy experiments in parallel. The first set of synthetic data was generated with the following parameters. Graphs of bacteria velocity and run duration together with tumbling angle and tumbling duration were plotted.
 Running Phase
Bacteria move at constant velocity v in direction θ for a period of time t.
 v drawn from Gaussian distribution of mean v_{0}=10μm/s and standard deviation σ_{1}=v_{0}/10.
 t drawn from Gaussian distribution of mean t_{0}=1s and standard deviation σ_{2}=t_{0}/10.
 Rotating Phase
Bacteria stop for a period of time T and rotate by an angle α.
 T drawn from Gaussian of mean T_{r}=0.1s and standard deviation σ_{r}=T/10.
 α drawn from Von Mises distribution of mean α_{0}=0 and parameter β=1.
 Useful mfile
Random number generator. This generates distributions including the normal and von Mises distributions. Save as randraw.m in the same folder as your model.
 MATLAB Code
 Model Construction of Bacteria Motility
Synthetic Simulations
 Generation of Realistic Synthetic Data
Realistic synthetic data was generated to model the random walk of a single bacterium. Using the previously constructed model the run of a bacteria was simulated over 5 minutes. A simple movie was created. Coordinate data was stored for the purpose of data analysis. Another model was built with unrealistic distributions.
 MATLAB Code

