Awesome Scientific Writing – Massive Collection of Resources

Scientific writing can extend beyond LaTeX, made possible by formats,
such as
Markdown (and its many flavours),
reStructuredText and
Jupyter notebooks.

🔖 means ability to seamlessly cite references.

🔗 means ability to cross-reference figures and sections within the
document.

Contents

• Word Processors
• Bibliography
• Illustrations
• Converters and Filters
• Spell Checking and Linting
• Templates
  • Articles
  • Presentations
  • Books
• Tutorials

Word Processors

• Atom – Popular IDE with Markdown support.
  • Markdown Preview Enhanced for Atom – Pandoc
    integration and utilities for Atom.
  • Autocomplete BibTeX for Atom – BibTeX support for Atom.
• Marktext – Markdown text editor.
• R Studio – IDE for R.
  • bookdown – R package to facilitate writing books and long-form articles, reports with R Markdown 🔖 🔗.
  • R Markdown – R package to write R next to Markdown
    🔖
    🔗.
• Vim – Command line text editor.
  • fzf-bibtex – BibTeX source
    with Vim integration which uses fzf (a fuzzy finder implemented in Go).
  • vim-pandoc – Pandoc integration and utilities for Vim.
  • vim-pandoc-syntax – Pandoc syntax highlighting for Vim.
• Visual Studio Code – Popular IDE with Markdown support.
  • Markdown All in One – Extension for enhanced
    Markdown support in VSCode, such as preview and auto completion to name a few.
• Zettlr – Markdown editor which
  integrates CSL, BibLaTeX, Pandoc and many other tools
  🔖 🔗.

Bibliography

Reference managers to generate citations, BibTeX, and BibLaTeX files.

• Citation Style Language (CSL) styles – Crowdsourced
  repository with over 9000 free CSL citation styles and an online
  editor to create new ones.
• JabRef – Open source bibliography reference manager.
• Zotero – FOSS tool to collect, organize, cite, and
  share research.
  • Better BibTeX for Zotero – Enhanced
    BibTeX / BibLaTeX integration for Zotero.
  • ZotFile for Zotero – Enhanced PDF file management for Zotero.
• ZoteroBib – Online bibliography reference manager.

Illustrations

Drawing illustrations themselves has driven many a scientist mad. Fortunately,
there are formal languages with which one can create beautiful graphics.

• diagrams.net – Open source, online, desktop and
  container deployable diagramming software.
• graphviz – Visualization software for graphs and
  networks which uses a domain-specific DOT language.
• Mermaid Live Editor – Define simple diagrams instead of drawing them.
• Vega Lite – Define charts and more complex diagrams.
• PlantUML – Define UML diagrams instead of drawing them.

Converters and Filters

Supplementary files and tools.

• Cicero – Python package which renders HTML presentations
  from Markdown source using remark or reveal.js 🔗.
• docutils – Python package which can
  convert reStructuredText into various formats and provides command-line
  tools to do it 🔗.
• Jupyter Book – A static site generator which converts
  a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website.
• MyST – Markedly Structured Text,
  a superset of CommonMark markdown with reStructuredText like features.
• nbconvert – Convert Jupyter
  notebooks into reveal.js presentations, PDF, HTML, Markdown,
  reStructuredText and more.
  • bookbook – Experimental Python
    package which extends nbconvert and adds the ability to cross reference
    within and across notebooks 🔗.
  • ipypublish – Workflow for
    creating and editing publication ready scientific reports and presentations,
    from one or more Jupyter Notebooks, without leaving the browser 🔖
    🔗.
• pandoc – Haskell library for converting from
  one markup format to another, and a command-line tool that uses this
  library 🔖 🔗.
  • Academic Markdown – Python wrapper over Pandoc with specialized extensions to parse certain
    elements, making it a superset of Pandoc Markdown flavour 🔖
    🔗.
  • Pandoc filters – List of
    addons to pandoc which implement extra features such as citations and
    cross-references.
  • Panflute – Pythonic alternative
    to John MacFarlane’s pandocfilters.

Spell Checking and Linting

• GNU Aspell – Command line spell checker.
• Hunspell – Command line spell checker.
• LanguageTool – Open source grammar, style and
  spell Checker.
• Markdown lint tool – Markdown linter.
• proselint – Linter for prose.
• remarklint – Markdown linter.
• restructuredtext-lint – reStructuredText linter.
• textlint – Pluggable linting tool for text
  and Markdown.
• textidote – Spelling, grammar and
  style checking on LaTeX documents.
• Vale – Free, open-source linter for
  prose built with speed and extensibility in mind.
• write-good – Naive linter for English
  prose.

Templates

Reusable minimalist examples.

Articles

• Pandoc Markdown-LaTeX
  Boilerplate – Demonstrate
  how to integrate Pandoc with an existing LaTeX template which
  requires some boilerplate code (i.e. LaTeX preamble), thus avoiding the
  latexmk dependency.
• scientific-markdown – Example
  for use of Markdown for scientific publications using Pandoc and
  latexmk.
• Steve’s R Markdown Templates – Academic manuscript, memos, Beamer presentation, syllabus and CV.

Presentations

• pandoc-starter – Templates for
  articles, Beamer presentations etc. using Markdown files and Makefiles for
  getting started with Pandoc.
• slides – Demo for generating reveal.js
  presentations using Pandoc.

Books

• bookdown-demo – Minimal
  example of a book based on R Markdown and bookdown.
• Eisvogel – Clean academic pandoc LaTeX template.
• Template for writing a PhD thesis in
  Markdown – Clean
  organization of files to provide a framework for writing a PhD thesis in
  mostly Markdown with a little bit of LaTeX, and compiled with Pandoc.

Tutorials

How to generate articles and presentations for scientific purposes.

• Book on Riemann solvers – This
  example uses a custom nbconvert template and shows how to store your
  notebooks with no output (for version control) while automatically executing
  them before running bookbook, so that PDF and HTML versions include the
  output.
• Dennis Tenen and Grant Wythoff – Sustainable Authorship in Plain Text using Pandoc and Markdown.
• Katrin Leinweber’s Ph.D.
  thesis – Automated
  work flow involving several tools, but primarily Pandoc, latexmk and
  Academic Markdown.
• Scott Selisker – Plain Text Workflow for Academic Writing with Atom.
• Teaching and learning with
  Jupyter – Book
  written in R Markdown, bookdown and also rendered as HTML, PDF and
  EPUB.
• Writing scientific papers for ACPD using Emacs
  Org-mode – Detailed
  tutorial on authoring a paper by seamlessly integrating with LaTeX
  commands within Org-mode.