IGEM:IMPERIAL/2008/Prototype/Drylab/Data Analysis/Gather Data
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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 v0=10μm/s and standard deviation σ1=v0/10.
- t drawn from Gaussian distribution of mean t0=1s and standard deviation σ2=t0/10.
- Rotating Phase
Bacteria stop for a period of time T and rotate by an angle α.
- T drawn from Gaussian of mean Tr=0.1s and standard deviation σr=T/10.
- α drawn from Von Mises distribution of mean α0=0 and parameter β=1.
- Useful m-file
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
- 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