first commit

README.md

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-# Markdown_for_papers
+# Markdown for papers
 
+== Taken from:
+
+https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8
+
+
+Another good example, dat project paper:
+https://github.com/datproject/docs
+
+== how does it work?
+
+The paper is edited in paper.md, and the converted into latex and pdf by [pandoc](https://pandoc.org/)
+
+
+== Paper generation
+
+```
+python3 conversion_script.py
+```

conversion_script.py

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+#!/usr/bin/python3
+
+#script using pandoc and pandoc-citeproc to transform a markdown file into a latex "paper"
+#Taken from
+#https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8
+
+from subprocess import call
+
+call(["pandoc", "--filter", "pandoc-citeproc", "--bibliography=paper.bib", "--variable", "classoption=twocolumn", "--variable", "papersize=a4paper", "-s", "paper.md", "-t", "latex", "-o", "paper.tex"])
+call(["pandoc", "--filter", "pandoc-citeproc", "--bibliography=paper.bib", "--variable", "classoption=twocolumn", "--variable", "papersize=a4paper", "-s", "paper.md", "-o", "paper.pdf"])
+

paper.bib

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+
+@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}
+}

paper.md

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+---
+title: "Pizza - A Carbohydrate Based Substrate For Tomato Delivery"
+date: "May 2017"
+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](https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/adaaa9b5c19460d3be42021ef0c1b8e11a8d38fe/pizza.png)
+
+# Algorithm
+
+$$f(x)=pizza^2$$
+
+# References

paper.tex

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+\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
+}{}
+\PassOptionsToPackage{hyphens}{url} % url is loaded by hyperref
+\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{https://gist.github.com/maxogden/97190db73ac19fc6c1d9beee1a6e4fc8/raw/adaaa9b5c19460d3be42021ef0c1b8e11a8d38fe/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}