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Mariano Bernaldo 3 years ago
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  1. 20
      README.md
  2. 11
      conversion_script.py
  3. 11
      paper.bib
  4. 19
      paper.md
  5. BIN
      paper.pdf
  6. 106
      paper.tex

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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
```

11
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"])

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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}
}

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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

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paper.pdf

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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}
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