Scientific Writing

Awesome Scientific Writing Awesome

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

πŸ”– means ability to seamlessly cite references.

πŸ”— means ability to cross-reference figures and sections within the document.

Word Processors

Bibliography

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

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 πŸ”—.
  • docutils - Python package which can convert reStructuredText into various formats and provides command-line tools to do it πŸ”—.
  • 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 πŸ”—.
  • ipypublish - Workflow for creating and editing publication ready scientific reports and presentations, from one or more Jupyter Notebooks, without leaving the browser πŸ”– πŸ”—.
  • pandoc - Haskell library for converting from one markup format to another, and a command-line tool that uses this library πŸ”– πŸ”—.
  • Academic Markdown - Python wrapper over Pandoc with specialized extensions to parse certain elements, making it a superset of Pandoc Markdown flavour πŸ”– πŸ”—.
  • 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

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

Tutorials

How to generate articles and presentations for scientific purposes.

Other Awesome Lists

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