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Fundamental Limits on the Rate of Bacterial Growth

DOI

Branches

This repository contains three branches -- master, gh-pages, and publication. The master branch contains the entire project history for start to finish and includes code and data that were exploratory or may not have made it into the final publication as well as the LaTeX document files. The gh-pages branch hosts all files associated with the paper website and contains the source files for the final compiled dataset as well as all scripts used for the figure generation. The final branch, publication (where you are now) strikes a middle ground between master and gh-pages. This branch contains all data and code used to generate figures, clean and process data, and compute estimations as necessary. This branch should be sufficient to reproduce everything presented in this work.

Installation

To run the code used in this work, you will need to install the prot module. prot is a custom Python package written specifically for this project and contains an array of functions used for everything from stylizing the plots to computing cell volumes as a function of growth rate. The software module itself can be installed locally by executing the command in the root directory,

pip install -e ./

When installed, a new folder prot.egg-info will be made in the root directory and is necessary to run any of the code.

PathwayTools

A key component of our work is scraping the EcoCyc database to associated individual proteins present in the datasets with the associated complexes. In order to do so, we used the PathwayTools software API. In order to run this part of the analysis (code/processing/ecocyc_subunit_munging/munge.py), you must have an active PathwayTools license.

Repository Architecture

This repository is broken up into several directories and subdirectories. Please see each directory for information regarding each file.

code

All Python code used in this work is located here and is written to be executed from its local directory. This directory contains two subdirectories in which the code is organized.

  1. processing | All code that was used in the cleaning of the raw datasets, interaction with databases, and collation of the complete datasets. This directory is broken up further into directories associated with each individual dataset or process.
  2. figures | All code used to generate the figures, both main text and supplemental. The scripts are written to be executed from this directory.

data

This self-explanatory folder contains all of the data, both raw and processed, used in this research.

License

All creative work (text, plots, images, etc.) are licensed under the Creative Commons CC-BY 4.0 license. All software is distributed under the standard MIT license as follows:

Copyright (c) 2020 The Authors

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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Repository for our project on exploring fundamental limits to bacterial growth

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