jchassoul · May 16, 2018 02:04 · May 5, 2017 · May 5, 2017 · May 5, 2017 · May 5, 2017
diff --git a/paper.md b/paper.md
@@ -10,7 +10,7 @@ Pizza (@pizza2000identification) is an understudied yet widely utilized implemen
 
 # Diagram
 
-![It's Pizza](pizza.png)
+![It's Pizza](https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/adaaa9b5c19460d3be42021ef0c1b8e11a8d38fe/pizza.png)
 
 # Algorithm
 

diff --git a/readme.md b/readme.md
@@ -30,7 +30,7 @@ The `pandoc-citeproc` filter will automatically generate a references section fo
 
 First you can grab some Bibtex references from Google Scholar and throw them in a `paper.bib` file:
 
-![](bibtex.png)
+![](https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/adaaa9b5c19460d3be42021ef0c1b8e11a8d38fe/bibtex.png)
 
 Then when you render the paper references will get converted automatically if you cite them using the identifier from the bibtex in Markdown like this:
 

diff --git a/bibtex.png b/bibtex.png
diff --git a/paper.md b/paper.md
@@ -1,12 +1,19 @@
 ---
-title: "Pizza - A Carbohydrate Based Substrate For Tomato Emulsion Delivery"
+title: "Pizza - A Carbohydrate Based Substrate For Tomato Delivery"
 date: "May 2017"
-author: "Maxwell Ogden"
+author: "Maxwell Ogden, Pizza Enthusiasts Institute"
 ---
 
-
 # Abstract
 
 Pizza (@pizza2000identification) is an understudied yet widely utilized implement for delivering in-vivo *Solanum lycopersicum* based liquid mediums in a variety of next-generation mastications studies. Here we describe a de novo approach for large scale *T. aestivum* assemblies based on protein folding that drastically reduces the generation time of the mutation rate.
 
+# Diagram
+
+![It's Pizza](pizza.png)
+
+# Algorithm
+
+$$f(x)=pizza^2$$
+
 # References
diff --git a/paper.pdf b/paper.pdf
diff --git a/paper.txt b/paper.txt
@@ -0,0 +1,105 @@
+\documentclass[a4paperpaper,twocolumn]{article}
+\usepackage{lmodern}
+\usepackage{amssymb,amsmath}
+\usepackage{ifxetex,ifluatex}
+\usepackage{fixltx2e} % provides \textsubscript
+\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
+  \usepackage[T1]{fontenc}
+  \usepackage[utf8]{inputenc}
+\else % if luatex or xelatex
+  \ifxetex
+    \usepackage{mathspec}
+  \else
+    \usepackage{fontspec}
+  \fi
+  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
+\fi
+% use upquote if available, for straight quotes in verbatim environments
+\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
+% use microtype if available
+\IfFileExists{microtype.sty}{%
+\usepackage{microtype}
+\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
+}{}
+\usepackage[unicode=true]{hyperref}
+\hypersetup{
+            pdftitle={Pizza - A Carbohydrate Based Substrate For Tomato Delivery},
+            pdfauthor={Maxwell Ogden, Pizza Enthusiasts Institute},
+            pdfborder={0 0 0},
+            breaklinks=true}
+\urlstyle{same}  % don't use monospace font for urls
+\usepackage{graphicx,grffile}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+\IfFileExists{parskip.sty}{%
+\usepackage{parskip}
+}{% else
+\setlength{\parindent}{0pt}
+\setlength{\parskip}{6pt plus 2pt minus 1pt}
+}
+\setlength{\emergencystretch}{3em}  % prevent overfull lines
+\providecommand{\tightlist}{%
+  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
+\setcounter{secnumdepth}{0}
+% Redefines (sub)paragraphs to behave more like sections
+\ifx\paragraph\undefined\else
+\let\oldparagraph\paragraph
+\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
+\fi
+\ifx\subparagraph\undefined\else
+\let\oldsubparagraph\subparagraph
+\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
+\fi
+
+% set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+
+
+\title{Pizza - A Carbohydrate Based Substrate For Tomato Delivery}
+\author{Maxwell Ogden, Pizza Enthusiasts Institute}
+\date{May 2017}
+
+\begin{document}
+\maketitle
+
+\section{Abstract}\label{abstract}
+
+Pizza (Pizza et al. (2000)) is an understudied yet widely utilized
+implement for delivering in-vivo \emph{Solanum lycopersicum} based
+liquid mediums in a variety of next-generation mastications studies.
+Here we describe a de novo approach for large scale \emph{T. aestivum}
+assemblies based on protein folding that drastically reduces the
+generation time of the mutation rate.
+
+\section{Diagram}\label{diagram}
+
+\begin{figure}
+\centering
+\includegraphics{pizza.png}
+\caption{It's Pizza}
+\end{figure}
+
+\section{Algorithm}\label{algorithm}
+
+\[f(x)=pizza^2\]
+
+\section*{References}\label{references}
+\addcontentsline{toc}{section}{References}
+
+\hypertarget{refs}{}
+\hypertarget{ref-pizza2000identification}{}
+Pizza, Mariagrazia, Vincenzo Scarlato, Vega Masignani, Marzia Monica
+Giuliani, Beatrice Arico, Maurizio Comanducci, Gary T Jennings, et al.
+2000. ``Identification of Vaccine Candidates Against Serogroup B
+Meningococcus by Whole-Genome Sequencing.'' \emph{Science} 287 (5459).
+American Association for the Advancement of Science: 1816--20.
+
+\end{document}
diff --git a/pizza.png b/pizza.png
diff --git a/readme.md b/readme.md
@@ -4,6 +4,8 @@ Markdown is the most common format for writing on GitHub, and is what I use for
 
 ![markdown example](https://gist.githubusercontent.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/c127b99eddbd3491114aefaaa60a124e566d77a5/markdown.png)
 
+The above example is from the [Dat Paper](https://github.com/datproject/docs/tree/master/papers).
+
 ### 1. Install Pandoc
 
 [Pandoc](https://en.wikipedia.org/wiki/Pandoc) is a great tool for converting between different print formats. In this case pandoc will handle these conversions for us, all in one command:
@@ -30,6 +32,26 @@ First you can grab some Bibtex references from Google Scholar and throw them in
 
 ![](bibtex.png)
 
-Then when you render the paper references will get converted like this:
+Then when you render the paper references will get converted automatically if you cite them using the identifier from the bibtex in Markdown like this:
+
+```
+The seminal work [@pizza2000identification]
+```
+
+### 4. Render it
+
+Once you have `.md` and `.bib` files you can generate a PDF like this:
+
+```
+pandoc --filter pandoc-citeproc --bibliography=paper.bib --variable classoption=twocolumn --variable papersize=a4paper -s paper.md -o paper.pdf
+```
+
+Or generate the intermediate Latex source like this:
+
+```
+pandoc --filter pandoc-citeproc --bibliography=paper.bib --variable classoption=twocolumn --variable papersize=a4paper -s paper.md -t latex -o paper.txt
+```
 
+### 5. Upload it
 
+Now you're ready to post the `.txt`, `.bib`, `.pdf` and `.md` files on a pre-print server, ideally with a CC0 public domain dedication license for maximum openness, and upload it to GitHub so others can access and re-use your research!
diff --git a/paper.bib b/paper.bib
@@ -0,0 +1,10 @@
+@article{pizza2000identification,
+  title={Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing},
+  author={Pizza, Mariagrazia and Scarlato, Vincenzo and Masignani, Vega and Giuliani, Marzia Monica and Arico, Beatrice and Comanducci, Maurizio and Jennings, Gary T and Baldi, Lucia and Bartolini, Erika and Capecchi, Barbara and others},
+  journal={Science},
+  volume={287},
+  number={5459},
+  pages={1816--1820},
+  year={2000},
+  publisher={American Association for the Advancement of Science}
+}
diff --git a/paper.md b/paper.md
@@ -0,0 +1,12 @@
+---
+title: "Pizza - A Carbohydrate Based Substrate For Tomato Emulsion Delivery"
+date: "May 2017"
+author: "Maxwell Ogden"
+---
+
+
+# Abstract
+
+Pizza (@pizza2000identification) is an understudied yet widely utilized implement for delivering in-vivo *Solanum lycopersicum* based liquid mediums in a variety of next-generation mastications studies. Here we describe a de novo approach for large scale *T. aestivum* assemblies based on protein folding that drastically reduces the generation time of the mutation rate.
+
+# References
diff --git a/readme.md b/readme.md
@@ -1,5 +1,35 @@
 ## How to make a scientific looking PDF from markdown (with bibliography)
 
-Markdown is the most common format for writing on GitHub, and is what I use for all of my own documentation. It also exports to HTML and other convenient formats for reading on mobile devices. However, sometimes you want to export it as a PDF so that you can author scientific papers and export the formats that pre-print servers want.
+Markdown is the most common format for writing on GitHub, and is what I use for all of my own documentation. It also exports to HTML and other convenient formats for reading on mobile devices. However, sometimes you want to export it as a PDF so that you can author scientific papers and export the formats that pre-print servers like [arxiv.org](https://arxiv.org/) will accept.
+
+![markdown example](https://gist.githubusercontent.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/c127b99eddbd3491114aefaaa60a124e566d77a5/markdown.png)
+
+### 1. Install Pandoc
+
+[Pandoc](https://en.wikipedia.org/wiki/Pandoc) is a great tool for converting between different print formats. In this case pandoc will handle these conversions for us, all in one command:
+
+```
+Markdown -> Latex -> Latex Citeproc Bibliography Filter -> PDF
+```
+
+To install it on Mac OS using homebrew:
+
+```
+brew install pandoc pandoc-citeproc
+```
+
+### 2. Author your paper
+
+See `paper.md` for an example. You can use YAML frontmatter to specify variables that Pandoc will use as the variables in it's Latex template. To see the Latex template you can run `pandoc -D latex`.
+
+### 3. Create a bibliography
+
+The `pandoc-citeproc` filter will automatically generate a references section for you at the end of your document, and also replace all Markdown references an academic citation style.
+
+First you can grab some Bibtex references from Google Scholar and throw them in a `paper.bib` file:
+
+![](bibtex.png)
+
+Then when you render the paper references will get converted like this:
+
 
-![markdown example](https://gist.githubusercontent.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/c127b99eddbd3491114aefaaa60a124e566d77a5/markdown.png)
diff --git a/readme.md b/readme.md
@@ -2,4 +2,4 @@
 
 Markdown is the most common format for writing on GitHub, and is what I use for all of my own documentation. It also exports to HTML and other convenient formats for reading on mobile devices. However, sometimes you want to export it as a PDF so that you can author scientific papers and export the formats that pre-print servers want.
 
-![markdown example](https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/3a813fa7d80ebeff65c13be5f9678eb5ef461120/markdown.png)
+![markdown example](https://gist.githubusercontent.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/c127b99eddbd3491114aefaaa60a124e566d77a5/markdown.png)
diff --git a/markdown.png b/markdown.png
diff --git a/readme.md b/readme.md
@@ -2,4 +2,4 @@
 
 Markdown is the most common format for writing on GitHub, and is what I use for all of my own documentation. It also exports to HTML and other convenient formats for reading on mobile devices. However, sometimes you want to export it as a PDF so that you can author scientific papers and export the formats that pre-print servers want.
 
-![markdown example](markdown.png)
+![markdown example](https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/3a813fa7d80ebeff65c13be5f9678eb5ef461120/markdown.png)
diff --git a/markdown.png b/markdown.png
diff --git a/readme.md b/readme.md
@@ -0,0 +1,5 @@
+## How to make a scientific looking PDF from markdown (with bibliography)
+
+Markdown is the most common format for writing on GitHub, and is what I use for all of my own documentation. It also exports to HTML and other convenient formats for reading on mobile devices. However, sometimes you want to export it as a PDF so that you can author scientific papers and export the formats that pre-print servers want.
+
+![markdown example](markdown.png)