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: