Team:Imperial College/Appendices

Modelling Motility

• Data extraction algorithm. Obtains motility properties from trajectory data
• Generates trajectory based on generated parameters
• Generates first run of the trajectory, to be called by modelfit1.m
• Generates second run of the trajectory, to be called by modelfit2.m
• Generates parameters for the first run of cell trajectory
• Generates parameters for the second run of cell trajectory

Synthetic Video

• Random Number Generator
• Generation of Bacteria Shape Characteristics
• Generation of Bacteria Motility Characteristics
• Generation of Synthetic Video (Requires the above 2 files to run)

Probabilistic Methods

• Plots the posterior of (μ,σ) for a normal distribution
• Plots the posterior of λ for an exponential distribution

Modelling Growth

• The growth of bacteria at a constant growth rate
• Simulation of the Hill Function
• Nutrient concentration and nutrient as a function of time, both plotted against time
• The growth model (N.B. Here the concentration of nutrients with respect to time is assumed to follow the trend given by a piecewise function)
• The growth model that fits the experimental data
• M-file for generating a plot of results from wetlab
• Excel spread sheet of Data from experiment + a log graph of experimental results

Modelling Genetic Circuit

• ODE system describing constitutive gene expression
• Simulation file for constitutive gene expression
• ODE system describing simple model
• Simulation file for simple model
• ODE system describing more complex model
• Simulation file for more complex model
• PDF of working - simple model
• PDF of working - complex model
• Simulation file for modelling LacI repression of promoter before IPTG is introduced

Tutorials

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