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Awesome Scientific Writing

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

:bookmark: means ability to seamlessly cite references.

:link: 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
• Other Lists

Word Processors

• Marktext - Markdown text editor.
• R Studio - IDE for R.
  • bookdown - R package to facilitate writing books and long-form articles, reports with R Markdown :bookmark: :link:.
  • R Markdown - R package to write R next to Markdown :bookmark: :link:.
• 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.
  • Markdown Preview Enhanced - Pandoc integration and utilities.
• Zettlr - Markdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools :bookmark: :link:.

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.

• app.diagrams.net - Open source, online, desktop and container deployable diagramming software named draw.io.
• 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 :link:.
• docutils - Python package which can convert reStructuredText into various formats and provides command-line tools to do it :link:.
• 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.
• pandoc - Haskell library for converting from one markup format to another, and a command-line tool that uses this library :bookmark: :link:.
  • Academic Markdown - Python wrapper over Pandoc with specialized extensions to parse certain elements, making it a superset of Pandoc Markdown flavour :bookmark: :link:.
  • 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.
• Quarto - Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia :bookmark: :link:.

Spell Checking and Linting

• GNU Aspell - Command line spell checker.
• Hunspell - Command line spell checker.
• LanguageTool - Open source grammar, style and spell Checker.
• LanguageCheck - Analyses scientific LaTeX papers, suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences.
• 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.

• 3 frameworks into one — Write your next paper with R Studio! - Article provides an overview to a workflow that combines R Markdown (bookdown), Zotero (literature management), and Notion (note taking on research papers) to write academic papers.
• 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.
• Heads up! Quarto is here to stay. Immediately combine R & Python in your next document - Summary of the capabilities of Quarto, why to use it, and how it compares to R Markdown. Also contains tips for M1 Mac users on how to fix a common problem with reticulate.
• 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.
• Write your dissertation in RMarkdown - Step-by-step guide on creating a complex pdf document, including text, figures, references, images, formatting, and more.
• Writing scientific papers for ACPD using Emacs Org-mode - Detailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode.

Other Lists

• Awesome Jupyter
• Awesome LaTeX
• Awesome Markdown
• Delightful Open Science

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