Welcome to the GitHub repository for the MWC mutants project! This repository contains the entire project history as well as curated scripts to make reproducibility feasible.

This repository consists of three branches -- master, gh-pages, and publication. The master branch is the primary working branch the authors used during the research. It contains all project history, processing data scripts, preliminary figure scripts, and other exploratory data analysis files. The gh-pages brach contains all of the website files including hosting of the interactive figures. Finally, the publication branch (which you are reading this on) contains all final processed data, figure generating scripts, data analysis scripts, and the software module mut. If interested in reproducing the work in this publication, you can execute the scripts on this branch. Please see the individual directories for more information.

To reproduce this work, you will need to use the mut module -- a homegrown Python software package written explicitly for this work. The requirements can be installed by executing the following command using pip in the command line:

pip install -r requirements.txt

The software module itself can be installed locally by executing the command in the root directory,

pip install -e ./

We have written a file install.sh that performs both of these steps. To install, simply run

sh install.sh

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

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

The name says it all. This repository contains all code used in this work to analyze data and generate figures. It is broken up into several subdirectories which separate the scripts by function.

1. analysis | Contains all Python scripts which perform data analysis procedures. This includes parameter inference and calibration of various statistical models.
2. figures | Contains all Python scripts which perform data visualization procedures. This includes generation all main and supplementary text figures as well as the interactive figures on the paper website.
3. stan | Contains all inferential models and associated functions written in the Stan probabilistic programming language.
4. processing | This folder contains a single script (example_processing.py) that illustrates how processing of the raw data was performed. It is kept very generic such that only a few parameters at the top of the script need to be changed from experiment to experiment.

This directory contains all processed and simulated data used in this work. The raw flow cytometry data is stored on the CaltechDATA research data repository under the DOI: 10.22002/D1.1241.

This folder contains .pdf files of all main and supplementary text figures. No code exists in this directory.

This is the heart-and-soul of the repository. It contains a series of Python files which define the myriad functions used in the processing, analysis, and visualization of data associated with this work. Pleas navigate to the directory to see a description of its contents.

We tested a selection of functions we believe are critical to this work. This includes the gaussian gating routine for processing of flow cytometry, computation of MWC active probabilities, and scraping of processed datasets to collect only the accepted experiments. This repository is powered by Travis Continuous Integration which periodically runs the test functions to ensure that everything passes.

All creative works (writing, figures, etc) are licensed under the Creative Commons CC-BY 4.0 license. All software is distributed under the standard MIT license as follows

Copyright 2019 The Authors 

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of this software and associated documentation files (the "Software"), to deal
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
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The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

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