flux_parity

This repository houses all data and code used in the manuscript "An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State".

Directory Structure

This repository is broken down into an array of directories and subdirectories which help organize the code, data, and outputs. These directories are as follows

code

This directory contains all Python and JavaScript code needed to generate the figures in this work. Scripts needed to generate the interactive figures can be found in the js subdirectory.

data

This directory, unsurprisingly, contains all of the data used int he analysis for this work. As no data was directly generated by us for this paper, all of these data come from other sources. Credit is given as needed either in the filename or in the associated notes.

This directory contains several subdirectories.

• main_figure_data: Contains all data files (as .csv's) used for Figures 4 and 5 of the main text.

• supplement_figure_data: Contains all data files (as .csv's) used for the figures in the supplemental text.

• source_data: Contains all of the data obtained from individual papers. In all cases, these data were collated into the datasets present in main_figure_data and supplement_figure_data. An exxception is the file COG_assignment.txt which corresponds to our manual COG assignments as displayed in Figure S3(A).

docs

This directory contains all files used to generate the paper website. FOr most purposes, this directory can be ignored.

figures

This directory contains PDF files of all of the figures present in the manuscript as well as the HTML files of the interactive figures.

growth

This is a custom Python module used to perform the analysis in this work. It is composed of three submodules used for visualization (viz.py), numerical integration (integrate.py), and for definition of the models (model.py). This module is used extensively throughout the code present in this work, and many of the core functions are reewritten in JavaScript in figures/js/functions.js.

This module is dependent on Python 3.8+. The dependencies and their versions are included in the requirements.txt file in the root of this directory.

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 ./

License

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) 2022 Griffin Chure & Jonas Cremer

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.