Quarto

What is Quarto?

Quarto is an open-source scientific and technical publishing system that lets you create beautiful, reproducible, and fully integrated documents—from simple Markdown reports to complex books, websites, interactive notebooks, and presentations.

Developed by Posit (formerly RStudio), Quarto is designed to unify code, text, figures, citations, and computational workflows in a single, transparent format.

At a glance, Quarto is:

  • Reproducible — integrates code execution (Python, R, Julia, Observable JS), ensuring outputs and figures are always up to date
  • Flexible — produce PDFs, HTML documents, slides, books, scientific manuscripts, apps, dashboards, and websites
  • Simple — Markdown-based syntax that remains readable even without rendering
  • Fully programmable — supports Jupyter, knitr, and executable notebooks
  • Integrated with the scientific ecosystem — works seamlessly with Zotero, BibTeX, Typst, Pandoc, Git, and Zenodo
  • Open and extensible — customizable templates, filters, and Lua extensions
  • Publication-ready — ideal for reproducible reports, dynamic analyses, teaching materials, and scientific communication

Quarto brings together what researchers often struggle to combine: documentation, computation, citation, formatting, and publishing—into one coherent workflow.

Why Quarto?

Scientific writing is often fragmented: code in Jupyter notebooks, figures exported by hand, citations in reference managers, and reports assembled in Word or LaTeX. This leads to broken pipelines, inconsistent results, and irreproducible outputs.

Quarto solves these problems by providing:

  • Executable documents — the analysis, text, and figures live in the same file
  • Reproducible workflows — every figure and result can be regenerated with one command
  • Transparent provenance — anyone can see exactly how results were produced
  • Portable documents — the same .qmd source can render to HTML, PDF, DOCX, slides, and more
  • Version control compatibility — plain-text files integrate perfectly with Git
  • Easy collaboration — clean syntax, consistent formatting, and shared environments
  • Open science readiness — perfect for publishing reproducible reports on GitHub Pages, Zenodo, or institutional archives

In short: Quarto turns scientific documents into reproducible research artifacts, strengthening transparency and accelerating collaboration.

Installation

Installation instructions are available from: https://quarto.org/docs/get-started/.

The installation can be tested with

quarto --help

Exercise: Create a Basic Quarto Document

Goal: Learn how to create a simple reproducible Quarto report.

Instructions:

  1. Open the example examples/quarto/report.qmd and instect the content.

  2. Render the document:

    uv quarto render examples/quarto/python_example.qmd

  3. Use the preview functionality:

    uv quarto preview examples/quarto/python_example.qmd

Outcome: You have created a fully reproducible report with integrated code and figures.

Exercise: Cite References with Zotero / BBT

Goal: Use your Zotero library inside Quarto.

Instructions:

  1. Export your Zotero collection via Better BibTeX as references.bib.

  2. In your YAML header, add:

    bibliography: references.bib

  3. Cite something in the text:

    As shown in @smith2021, citation management is seamless.

  4. Render the document and verify the bibliography appears at the end.

Outcome: You can now use structured, reproducible citations in Quarto.

Further Reading

Slides