Data for "Signal Amplification in Synthetic Bacterial Communication"

The files provided here contain the data and Python code referenced in the PhD thesis entitled "Signal Amplification in Synthetic Bacterial Communication". Python analysis and simulation files are in the tar archive `analysis.tgz`, in which the top-level directories `platereader`, `microscopy`, and `omnitray-modeling` correspond respecting order to platereader experiments, microscopy experiments, and simulations. Microscopy data are stored in tar archives and are labeled by date codes as YYMMDD.tgz. When these archives are extracted to the directory `microscopy/data` they can be accessed by the `viewing_aquisitions.ipynb` or `200626_analysis.ipynb` Jupyter Notebooks. The time lapse microscopy images are unprocessed TIFF files. Raw and processed platereader data are in the `biotek_data.tgz` tar archive and related MCMC walker traces are in `mcmc_outputs.tgz'. The analysis code includes Jupyter Notebooks, Python modules, and SLURM job scripts. The job scripts are unchanged and unsuitable for the out-of-the box use. However, a user may need to adapt these scripts in order to perform processing or simulation before exploring data or generating figures in a Jupyter Notebook.