phd

This work is licensed under a Creative Commons Attribution 4.0 International License.

Contact

If you have any questions about the scientific material or the actual structure of this thesis repository please feel free to open an issue and I will respond as soon as I can.

Each chapter of the thesis has a Disqus discussion board at the bottom of each Chapter. If you'd like to have a more public conversation, please head there!

About

This repository contains all files used to generate my PhD thesis "The Molecular Biophysics of Evolutionary and Physiological Adaptation" defended at the California Institute of Technology (hopefully) on June 1, 2020. This includes all Python and Stan code used to generate figures, all markdown files used to actually write the thesis, and all HTML files and shell scripts used to generate the website and PDF versions of the thesis.

Repository Structure

docs

This folder contains all live files displayed on the associated thesis website http://gchure.github.io/phd. This folder is recognized by GitHub Pages which serves the web content. Everything in this folder is generated by executing make html in the repository root. There is nothing of direct use in this folder of the repository.

doks-theme

This folder contains all materials for the Doks website theme which is parsed and built using the Jekyll blogging framework. This theme was purchased and subsequently heavily modified to match my aesthetic requirements. If you are interested in using a similar theme for your project, please support the developers of the theme and purchase a license.

src

This folder houses and meat-and-potatoes of the actual PhD thesis. There are many subdirectories, which I outline below.

• chapter_0X | There is a single folder for each chapter of the thesis. Within each folder is a single markdown document for each portion of the chapter (e.g. section_01_abstract.md, section_02_model.md etc.). These files contain the text of the chapter.
  • figs | This folder contains PDF and PNG versions of all images used in that chapter.
  • code | This folder contains all Python and/or Stan files used in the generation of all quantitative figures of the chapter. Each script relies on the use of the phd custom software module which is described in the next section of this README file.
• frontmatter | This folder contains all of the thesis frontmatter markdown files including the abstract, acknowledgments, list of published contributions, and a lua filter that allows the use of short-captions for the PDF version of the thesis.
• styles | This folder contains the bibliography format used in this thesis (cell.csl) as well as a Pandoc markdown template which follows the guidelines provided by the Caltech Thesis website.

Outside of these directories, there is a smattering of other files that are used in the actual generation of the thesis. These are listed below.

• caltech_thesis.cls | This is the LaTeX template file provided from the Caltech library.
• caltech.png | A high-resolution PNG file of the Caltech logo which is present on the PDF version of the thesis.
• metadata.yaml | A yaml file containing metadata about the thesis. This includes author name, thesis title, rights statement, and a variety of other configuration details for the HTML and PDF generation of the thesis.
• ref_formatting.yaml | This is a yaml file which contains configurations for how figure, equation, and template references should be displayed.
• ref_heading.md | A markdown file with a single line that reads # References. This is a hack I used to allow chapter-level references for the website, but not for the PDF.
• references.bib | The bibliography file containing information of all references used in the thesis.
• simple_letters.ist | A index style file provided by the Caltech Library.

To execute much of the code in the chapter_0X/code directories, you must have the data sets downloaded locally to a src/data folder. Due to size constraints, these data have not been directly stored on GitHub and you must download them externally. These data are available via the CaltechDATA research data repository under the DOI: 10.22002/D1.1426.

phd

This is a custom Python package used in the analysis and generation of all figures presented in the thesis. If you want to regenerate any of the figures in this thesis, you will need to install this package locally. You can do so by executing the following command of the root directory of the repository.

pip install -e ./

Within the phd folder is a slew of Python modules. These modules serve the following functions.

• __init__.py | An init file used to collect the package for import.
• _fit_bivariate_normal_AstroML.py | This contains several functions adapted from AstroPy to facilitate fitting of a bivariate gaussian distribution to flow cytometry data for reproducible gating.
• bayes.py | Contains myriad functions for performing Bayesian statistical inference including interaction with the Stan probabalistic programming language.
• flow.py | A variety of functions for interacting with flow cytometry data.
• image.py | A variety of functions for processing image files including segmentation, filtering, and measurement of object properties.
• io.py | A slew of functions for file IO.
• mscl.py | A set of highly-custom functions used in the analysis of single-cell microscopy data discussed in Chapters 5 and 9 of the thesis.
• stats.py | Helper functions for easy calculation of statistical properties including Highest Probability Density intervals which are reported frequently throughout the thesis.
• thermo.py | Contains two classes MWC and SimpleRepression which define the thermodynamic models discussed in the bulk of the thesis.
• viz.py | A collection of functions which format matplotlib and Altair plots to my personal style.

dst

This directory contains the PDF version of the thesis and is populated by executing make pdf from the root directory. This folder exists solely so I didn't confuse myself on where the most recent version of the PDF lived.

./

Outside of the directories described above, there are a variety of other files. Below, I describe the purpose of each one.

• _config.yml | A configuration file for website generation via Jekyll.
• .gitignore | A text file with information of files that Git should ignore.
• abstract.md | A markdown file that specifies the abstract page of the thesis website.
• acknowledgements.md | Just like abstract.md, this file generates the webpage for the acknowledgments
• chapter_0X.md | Markdown files that contain all information necessary to build the chapter pages of the thesis website.
• coppyfigs.sh | A shell script to be executed by the makefile which copies all .png versions of the figures from the src/chapter_0X/figs/ folder and copies them to the appropriate place in the docs/ folder.
• favicon.ico, Gemfile, Gemfile.lock | Files which specify details about the Ruby requirements necessary to build the website.
• index.md | The homepage of the thesis website.
• Makefile | A makefile used to assemble the thesis in to a human-friendly form. This file can be executed to make either the website components (make html) or the PDF components (make pdf) of the thesis.
• setup.py | Python file necessary for installation of the phd Python module.

License

All creative work in this repository is licensed under a Creative Commons CC-BY 4.0 Attribution license. All software is issued under a standard MIT license as follows:

Copyright 2021 Manuel Razo-Mejia

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.