[[
wikihub
]]
Search
⌘K
Explore
People
For Agents
Sign in
Explore
People
For Agents
Sign in
@harrisonqian / Awesome / wiki/miscellaneous/scientific-writing.md
Suggest edit
Cancel
Submit suggestion
Title
Name
Note
--- visibility: public --- # Scientific Writing **repo:** [writing-resources/awesome-scientific-writing](https://github.com/writing-resources/awesome-scientific-writing) **category:** [[miscellaneous|Miscellaneous]] **related:** [[free-programming-books|Free Programming Books]] · [[markdown|Markdown]] --- # Awesome Scientific Writing [](https://github.com/sindresorhus/awesome) > Scientific writing can extend beyond LaTeX, made possible by formats, > such as > [Markdown](https://daringfireball.net/projects/markdown/) (and its many flavours), > [reStructuredText](https://docutils.sourceforge.io/rst.html) and > [Jupyter notebooks](https://jupyter.org/). :bookmark: means ability to **seamlessly cite references**. :link: means ability to **cross-reference figures and sections within the document**. ## Contents - [Word Processors](#word-processors) - [Bibliography](#bibliography) - [Illustrations](#illustrations) - [Converters and Filters](#converters-and-filters) - [Spell Checking and Linting](#spell-checking-and-linting) - [Templates](#templates) - [Articles](#articles) - [Books](#books) - [Tutorials](#tutorials) - [Other Lists](#other-lists) ## Word Processors - [Marktext](https://github.com/marktext/marktext) - [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) text editor. - [R Studio](https://github.com/rstudio/rstudio) - IDE for R. - [bookdown](https://github.com/rstudio/bookdown) - R package to facilitate writing books and long-form articles, reports with R [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) :bookmark: :link:. - [R Markdown](https://rmarkdown.rstudio.com/) - R package to write R next to [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) :bookmark: :link:. - [Vim](https://www.vim.org/) - Command line text editor. - [fzf-bibtex](https://github.com/msprev/fzf-bibtex/#readme) - BibTeX source with Vim integration which uses fzf (a fuzzy finder implemented in Go). - [vim-pandoc](https://github.com/vim-pandoc/vim-pandoc) - Pandoc [integration](/@harrisonqian/awesome/wiki/platforms/integration) and utilities for Vim. - [vim-pandoc-syntax](https://github.com/vim-pandoc/vim-pandoc-syntax) - Pandoc syntax highlighting for Vim. - [Visual Studio Code](https://code.visualstudio.com/) - Popular IDE with [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) support. - [Markdown All in One](https://github.com/yzhang-gh/vscode-markdown/#readme) - Extension for enhanced Markdown support in VSCode, such as preview and auto completion to name a few. - [Markdown Preview Enhanced](https://github.com/shd101wyy/markdown-preview-enhanced) - Pandoc integration and utilities. - [Zettlr](https://www.zettlr.com/) - [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/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](https://editor.citationstyles.org/) - Crowdsourced repository with over 9000 free CSL citation styles and an online editor to create new ones. - [JabRef](https://www.jabref.org/) - Open source bibliography reference manager. - [Zotero](https://www.zotero.org/) - FOSS tool to collect, organize, cite, and share research. - [Better BibTeX for Zotero](https://retorque.re/zotero-better-bibtex/) - Enhanced BibTeX / BibLaTeX integration for Zotero. - [ZoteroBib](https://zbib.org/) - 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](https://app.diagrams.net/) - Open source, online, desktop and container deployable diagramming software named draw.io. - [graphviz](https://graphviz.org/) - Visualization software for graphs and networks which uses a domain-specific DOT language. - [Mermaid Live Editor](https://mermaid-js.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/mermaid-live-editor/) - Define simple diagrams instead of drawing them. - [Vega Lite](https://vega.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/vega-lite/examples/) - Define charts and more complex diagrams. - [PlantUML](https://plantuml.com/) - Define UML diagrams instead of drawing them. ## Converters and Filters Supplementary files and tools. - [Cicero](https://cicero.xyz/) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python) package which renders HTML presentations from Markdown source using remark or reveal.js :link:. - [docutils](https://docutils.sourceforge.io/docs/) - [Python](/@harrisonqian/awesome/wiki/programming-languages/python) package which can convert reStructuredText into various formats and provides command-line tools to do it :link:. - [Jupyter Book](https://jupyterbook.org/en/stable/) - A static site generator which converts a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website. - [MyST](https://myst-parser.readthedocs.io/en/latest/) - Markedly Structured Text, a superset of CommonMark markdown with reStructuredText like features. - [nbconvert](https://nbconvert.readthedocs.io/en/latest/) - Convert [Jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) notebooks into `reveal.js` presentations, PDF, HTML, Markdown, reStructuredText and more. - [pandoc](https://pandoc.org/MANUAL) - [Haskell](/@harrisonqian/awesome/wiki/programming-languages/haskell) library for converting from one markup format to another, and a command-line tool that uses this library :bookmark: :link:. - [Pandoc filters](https://github.com/jgm/pandoc/wiki/Pandoc-Filters) - List of addons to pandoc which implement extra features such as citations and cross-references. - [Panflute](http://scorreia.com/software/panflute/) - Pythonic alternative to John MacFarlane's pandocfilters. - [Quarto](https://quarto.org) - Compile R [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown), and [Jupyter](/@harrisonqian/awesome/wiki/miscellaneous/jupyter) Notebooks to PDFs, Slides and Websites. Supports R, [Python](/@harrisonqian/awesome/wiki/programming-languages/python), and [Julia](/@harrisonqian/awesome/wiki/programming-languages/julia) :bookmark: :link:. ## Spell Checking and Linting - [GNU Aspell](http://aspell.net/) - Command line spell checker. - [Hunspell](http://hunspell.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/) - Command line spell checker. - [LanguageTool](https://languagetool.org/) - Open source grammar, style and spell Checker. - [LanguageCheck](https://github.com/JohannesBuchner/languagecheck) - Analyses scientific [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) [papers](/@harrisonqian/awesome/wiki/computer-science/papers), suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences. - [Markdown lint tool](https://github.com/markdownlint/markdownlint) - [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) linter. - [proselint](https://github.com/amperser/proselint) - Linter for prose. - [remarklint](https://github.com/remarkjs/remark-lint) - [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) linter. - [restructuredtext-lint](https://github.com/twolfson/restructuredtext-lint) - reStructuredText linter. - [textlint](https://textlint.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/) - Pluggable linting tool for text and Markdown. - [textidote](https://sylvainhalle.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/textidote/) - Spelling, grammar and style checking on LaTeX documents. - [Vale](https://github.com/errata-ai/vale) - Free, open-source linter for prose built with speed and extensibility in mind. - [write-good](https://github.com/btford/write-good) - Naive linter for English prose. ## Templates Reusable minimalist examples. ### Articles - [Paper Templates for [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) Pages](https://github.com/dev-onejun/paper-templates-for-github-pages) - [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown)-based templates for [papers](/@harrisonqian/awesome/wiki/computer-science/papers) and RESUME/CVs, publishing with [GitHub](/@harrisonqian/awesome/wiki/development-environment/github) Pages. ### Books - [bookdown-demo](https://github.com/rstudio/bookdown-demo/#readme) - Minimal example of a book based on R Markdown and bookdown. - [Eisvogel](https://github.com/Wandmalfarbe/pandoc-[latex](/@harrisonqian/awesome/wiki/miscellaneous/latex)-template) - Clean academic pandoc [LaTeX](/@harrisonqian/awesome/wiki/miscellaneous/latex) template. - [Template for writing a PhD thesis in Markdown](https://github.com/tompollard/phd_thesis_markdown#readme) - 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](/@harrisonqian/awesome/wiki/front-end-development/frameworks) into one — Write your next paper with R Studio!](https://blog.devgenius.io/write-your-whole-paper-in-r-it-is-better-77e1843f0c09) - Article provides an overview to a workflow that combines R [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown) (bookdown), Zotero (literature management), and Notion (note taking on research papers) to write academic [papers](/@harrisonqian/awesome/wiki/computer-science/papers). - [Book on Riemann solvers](https://github.com/clawpack/riemann_book/#readme) - 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](https://programminghistorian.org/en/lessons/sustainable-authorship-in-plain-text-using-pandoc-and-markdown) - Sustainable Authorship in Plain Text using Pandoc and [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown). - [Heads up! [Quarto](/@harrisonqian/awesome/wiki/miscellaneous/quarto) is here to stay. Immediately combine R & [Python](/@harrisonqian/awesome/wiki/programming-languages/python) in your next document](https://blog.devgenius.io/heads-up-quarto-is-here-to-stay-aa861ef87491) - Summary of the capabilities of [Quarto](/@harrisonqian/awesome/wiki/miscellaneous/quarto), why to use it, and how it compares to R [Markdown](/@harrisonqian/awesome/wiki/miscellaneous/markdown). Also contains [tips](/@harrisonqian/awesome/wiki/programming-languages/tips) for M1 Mac users on how to fix a common problem with reticulate. - [Write your dissertation in RMarkdown](https://ourcodingclub.[github](/@harrisonqian/awesome/wiki/development-environment/github).io/tutorials/rmarkdown-dissertation/) - Step-by-step guide on creating a complex pdf document, including text, figures, references, images, formatting, and more. - [Writing scientific [papers](/@harrisonqian/awesome/wiki/computer-science/papers) for ACPD using [Emacs](/@harrisonqian/awesome/wiki/editors/emacs) Org-mode](https://www.draketo.de/english/emacs/writing-papers-in-org-mode-acpd) - Detailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode. ## Other Lists - [Awesome Jupyter](https://github.com/markusschanta/awesome-jupyter/#renderingpublishingconversion) - [Awesome LaTeX](https://github.com/egeerardyn/awesome-LaTeX/#readme) - [Awesome Markdown](https://github.com/BubuAnabelas/awesome-markdown/#readme) - [Delightful Open Science](https://codeberg.org/teaserbot-labs/delightful-open-science) ### Contribute Contributions welcome! Read the [contribution guidelines](CONTRIBUTING.md) first.