Welcome to the research repository for our recent preprint "Stringent Control of Cytoplasmic and Membrane Densities Defines Regulation of Cell Geometry in Escherichia coli!" This repo houses all code and (almost) all data used for the findings reported in the work. Microscopy images are large (≈ 15GB) and hosted separately on the Stanford Research Data Repository accessible via doi:10.25740/mk520hp6879.
This repository is still in an active research phase and will be further developed over the course of the review process. Below is a brief summary of each subdirectory and what it houses.
It will not shock you to hear that this houses all code used in this work. This code is almost exclusively written in Python, though statistical models were defined in the Stan probabilistic programming language. Within this directory are several subdirectories as follows:
-
analysis: This directory houses all code used in the statistical analyses presented in this work. It is further broken down into segments for the inference of the model parameters and inference of the data parameters, primarily from our own experiments. -
processing: This directory houses scripts used in the processing and cleaning of literature data used in this work and in the processing of raw experimental measurements. -
visualization: This directory houses Python scripts used in generating all of the figures in this work.
This is where all of the (small) datasets used in this work live. It is broken down in to groups of literature data and our own measurements. Further documentation of each file and subdirectory will be refined after the review processes has completed.
This directory houses all of the figures used in the manuscript, usually separated by figure panel. As of now, this houses many different versions used in different stages of the manuscript.
This directory houses markdown files with media recipes and detailed step-by-step guides for the various experimental protocols performed in this work.
This project required the development of an independent software package, primarily
for the image processing. This module (named size) is packaged and documented
as a typical Python software package.
Installing this package is necessary to run effectively all of the code used in this work. To install locally via pip, you can run the following from the command line in the root directory:
pip install -e ./software/
All creative work (e.g. prose, artwork) is licensed under a CC-BY 4.0 license. The software herein is licensed under a standard MIT license, which reads as follows:
MIT License
Copyright (c) 2023 The Authors
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