IGEM:IMPERIAL/2008/Prototype/Drylab/Data Analysis/Gather Data

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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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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.

Gaussian distribution of Bacteria Motility
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

Synthetic Simulations

Modelled random walk of a single bacterium
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

Generation of Bacteria Run


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