Hello Quarto

BioC 2022

mine çetinkaya-rundel

mine.quarto.pub/hello-quarto-bioc

Acknowledgements


Julia Stewart Lowndes, Phd


Artwork by Allison Horst

Hello, Quarto?

Quarto unifies and extends
the R Markdown ecosystem

Quarto unifies and extends
the R Markdown ecosystem


unifies for people who love R Markdown


extends for people who don’t know R Markdown

Poll

slido.com / #quarto

Quarto is a new, open-source,
scientific and technical
publishing system

Quarto is a new, open-source,
scientific and technical
publishing system

the goal is to make the process of creating
and collaborating dramatically better

A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.

Quarto logo with all four quadrants labelled as Share, Collaborate, Teach, and Reimagine.

Share

A Venn diagram with three circles -- education, research, and development. At the intersection is a blue heart with the word compassion.

Penguin with nametag that says "Mine"

The R Markdown ecosystem

Hex logos for various packages from the R Markdown ecosystem.

Quarto: Next generation R Markdown

Quarto logo.

Quarto highlights

One quadrant of the Quarto logo. Consistent implementation of attractive and handy features across outputs: tabsets, code-folding, syntax highlighting, etc.

Two quadrants of the Quarto logo. More accessible defaults as well as better support for accessibility

Three quadrants of the Quarto logo. Guardrails, particularly helpful for new learners: YAML completion, informative syntax errors, etc.

Four quadrants of the Quarto logo. Support for other languages like Python, Julia, Observable, and more via Jupyter engine for executable code chunks.

Quarto CLI orchestrates
each step of rendering

A schematic representing rendering of Quarto documents from .qmd, to knitr or jupyter, to plain text markdown, then converted by pandoc into any number of output types including html, PDF, or Word document.

Quarto makes moving between formats straightforward

Document

lesson-1.qmd

title: "Lesson 1"
format: html

Presentation

lesson-1.qmd

title: "Lesson 1"
format: revealjs

Website

_quarto.yml

project:
  type: website

website: 
  navbar: 
    left:
      - lesson-1.qmd

Quarto facilitates open sharing


Tooling that makes it easy to share what you do
with the world on the web is incredibly useful


It’s useful not just to you, but to the world
as it facilitates open sharing of knowledge
for learning and for reuse

Collaborate

Many scientists
use Python
😬

Poll

slido.com / #quarto

Quarto enables collaborating
across coding languages


_quarto.yml

contents:
  - section: in-development/index.qmd
    contents:
      - in-development/earthdata-access-demo.ipynb
      - in-development/nsidc/icesat2-cmr-onprem-vs-cloud.ipynb
      - in-development/lpdaac/lpdaac_ecostress_lste_kerchunk.ipynb
      - in-development/matlab-aws.qmd
      - in-development/earthdata-python-r-handoff.rmd  
  - section: contributing/onboarding.qmd
    contents: 
      - contributing/quarto-website-tutorial.md

Quarto enables contributing
from our current tools

Screenshot of RStudio IDE

Screenshot of Jupyter Lab

Screenshot of GitHub IDE

Screenshot of VS Code IDE

Teach

Quantifying
Art Historical
Narratives


Holland Stam

Art History +
Visual and Media Studies

Class of 2022

Duke University

Holland working at a table in the Broadhead Center, measuring an entry with a ruler.

Quantifying
Art Historical
Narratives


Holland Stam

Art History +
Visual and Media Studies

Class of 2022

Duke University

with Sara Lemus Hex logo for the package arthistory.

Holland working at a table in the Broadhead Center, measuring an entry with a ruler.

Quarto flattens the learning curve

A schematic showing many qmd files, going through Quarto, to generate an HTML, PDF, or Word document or more. The Quarto logo is depicted as a baseball a penguin is spinning.

Quarto can grow with learners in a profound way


A schematic showing many computing languages (R, Python, Julia, Observable, and more) going into many single qmd files, going through Quarto, to generate an HTML, PDF, or Word document or more. The Quarto logo is depicted as a baseball a penguin is spinning.

Reimagine

Because of Openscapes, I have renewed hope in how we can bring about a kinder future in science. I see a commitment in the open science community to bridging the gaps where we’ve left members of our community behind, and it inspires me.

Ileana Fenwick
University of North Carolina, Openscapes

Screenshot of a Quarto site that is a lab manual of shared practices

thefaylab.github.io/lab-manual/

Quarto enables collaborating
across coding comfort levels

RStudio IDE

Thank you

mine.quarto.pub/hello-quarto-bioc

Say hello to Quarto!

Two penguins. The orange one is holding the Quarto logo. The blue one is looking at the orange one.