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Collaborate on research papers with GitHub

 2 years ago
source link: https://techcommunity.microsoft.com/t5/educator-developer-blog/collaborate-on-research-papers-with-github/ba-p/2296894?WT_mc_id=DOP-MVP-4025064
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Collaborate on research papers with GitHub

Collaborate on research papers with GitHub

Published 04-27-2021 09:08 AM 552 Views

GitHub is well-known as a platform where software developers host their code and collaborate with their teams on a project. In this blog post, we'll show you how you can use the GitHub model to do the same thing and collaborate seamlessly on your research papers.



This blog post is co-authored with Ornella Altunyan, because we believe that GitHub is a great technology and tool to be used beyond pure software development.

Git, GitHub, and how it all works



The first thing you’ll want to do is set up Git. Git is the version control system that runs behind the scenes of any GitHub project—it’s what allows you to collaborate with others, go back to previous versions of your project, and view changes made by different members of your team. You may want to use Git from a command-line, but in the beginning, it might be easier to use the GitHub Desktop client.



Projects on GitHub are organized in repositories. You’ll create a new repository for your research paper, and choose who you want to have access. All your files, whether you’re using Markdown, LaTeX, or another typesetting or markup language (more on that later!) will live in this repository. You’ll want to clone the repository to your local machine, so that you have a copy of your files on your local machine.



The source of truth for your paper will live on the main branch of your repository – this branch is initialized when you create your repository. You can create multiple branches for different sections of your paper, and edit and merge them into your main branch when you’re finished. A commit is a snapshot of your repository at a given moment, and it might contain a set of changes that you’ve made to the information on a specific branch.



This is just a short introduction to all the features you can take advantage of when you use GitHub to collaborate on your research papers. Keep reading for more information, and a sample workflow that you can use to get started.



What should and should not be stored in Git



It is important to understand that GitHub is not a replacement for file storage, or a convenient storage for binary files. It was originally designed to be used as a source code repository, and thus it allows you to track changes between text documents. If you are planning on collaborating on Word documents, setting up a shared OneDrive location is a much better choice. For this reason, many people don’t consider GitHub to be a convenient collaboration platform for editing documents. However, scientists often write their papers in text format, most often – TeX or LaTeX. This makes it very convenient to use GitHub as a collaboration platform. It is one of the reasons we believe that GitHub is a very beneficial collaboration platform for scientists.

Why GitHub?



Using Git will give you many advantages:

LaTeX or Markdown?



Most scientists write their papers in LaTeX, mostly because it provides easy access to a lot of workflows in academia, like paper templates. There are also some good collaboration platforms specific to TeX, for example, Overleaf. However, it won't give you full control of your versioning and collaboration features like Git. 



Writing in LaTeX also requires quite a bit of overhead, meaning that many layout features are quite verbose, for example:

\subsection{Section 1}
\begin{itemize}
  \item Item 1
  \item Item 2
\end{itemize}

In the world of software development, there is a language for writing formatted text documents – Markdown. Markdown looks just like a plain text document. For example, the text above would be formatted like this:

## Section 1

* Item 1
* Item 2

This document is much easier to read as plain text, but it is also formatted into a nice looking document by Markdown processors. There are also ways to include TeX formulae into markdown using specific syntax.



In fact, I've been writing all of my blog posts and most text content in Markdown for a few years, including posts with formulae. For scientific writing, the great Markdown processor (as well as live editing environment) integrated with TeX is madoko – I highly recommend you check it out. You can use it from the web interface (which has GitHub integration), and there's also an open-source command-line tool to convert your markdown writing into either LaTeX, or directly to PDF.





While you may continue using LaTeX with Git, I encourage you to look into markdown-based writing options. By the way, if you have some writing in different formats, such as Microsoft Word documents, it can be converted to Markdown using a tool called pandoc.



Sample workflow



Main thing that git does is to allow you to structure your writing (whether it is code or scientific paper) into chunks called commits. Your code is tracked in the local repository, and once you have done some changes – you need to specifically commit them. Then, you can also synchronize your commits with others by using some remote common repository, called upstream.

Sounds complicated? When using GitHub Desktop most of the tasks are completely automated for you. Below we will describe the simplest way you can collaborate on a paper with your colleagues.

This is one example of a Git workflow you can use in conjunction with GitHub Desktop to collaborate on a research paper with your colleagues. There are several other ways that may serve your needs better—you may want to use the command line with VS Code, or edit your files on GitHub in the browser. Whatever method works for you is the best method, as long as you’re able to accomplish your goals.

Further reading and useful links

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