https://github.com/cremerlab/flux_parity

Complete history of the manuscript "An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State"

https://github.com/cremerlab/flux_parity

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Complete history of the manuscript "An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State"

https://github.com/cremerlab/flux_parity/blob/master/

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# `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](https://creativecommons.org/licenses/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.
```

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