diff --git a/FAQ.qmd b/FAQ.qmd index 8d2a240..db8dfb0 100644 --- a/FAQ.qmd +++ b/FAQ.qmd @@ -10,6 +10,6 @@ This notebook publication (or "notebook pub") is an experimental format we're te There is a comment section at the bottom of the [pub](index.ipynb), where you can read and contribute to any community discussion. Note that commenting requires a GitHub account and authorizing Giscus, a GitHub Discussions widget. -## 3. Can I join? +## 3. How can I contribute? We welcome improvements to this publication! Please see our guide for [contributing](CONTRIBUTING.qmd). diff --git a/_quarto.yml b/_quarto.yml index bbe89d4..7fd5f04 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -8,7 +8,6 @@ website: favicon: assets/logo_white.png # https://quarto.org/docs/websites/website-tools.html#favicon twitter-card: true # https://quarto.org/docs/websites/website-tools.html#twitter-cards open-graph: true # https://quarto.org/docs/websites/website-tools.html#open-graph - title: "Arcadia Science" navbar: title: false left: @@ -16,7 +15,7 @@ website: menu: - text: latest href: index.ipynb - - text: Paired residue prediction dependencies in ESM2 + - text: "{{< var pub.title >}}" href: index.ipynb right: - text: FAQ @@ -27,7 +26,7 @@ website: - icon: twitter-x href: https://twitter.com/arcadiascience - icon: github - href: https://github.com/Arcadia-Science/notebook-pub-template + href: https://github.com/{{< var pub.repo >}} logo: assets/logo_text.png logo-href: https://www.arcadiascience.com/ background: white @@ -42,7 +41,7 @@ website: - icon: twitter-x href: https://twitter.com/arcadiascience - icon: github - href: https://github.com/Arcadia-Science/notebook-pub-template + href: https://github.com/{{< var pub.repo >}} format: html: include-in-header: @@ -53,5 +52,5 @@ format: toc: true comments: giscus: - repo: Arcadia-Science/notebook-pub-template + repo: "{{< var pub.repo >}}" input-position: top diff --git a/_variables.yml b/_variables.yml new file mode 100644 index 0000000..5882b5f --- /dev/null +++ b/_variables.yml @@ -0,0 +1,3 @@ +pub: + repo: "Arcadia-Science/notebook-pub-template" + title: "Notebook pub template demo" diff --git a/assets/logo-animation.html b/assets/logo-animation.html index 28fa17b..505edc2 100644 --- a/assets/logo-animation.html +++ b/assets/logo-animation.html @@ -10,7 +10,7 @@ video.muted = true; video.playsInline = true; video.loop = false; - video.playbackRate = 0.8; + video.playbackRate = 1.0; const source = document.createElement("source"); diff --git a/index.ipynb b/index.ipynb index 8c76ae8..feade5c 100644 --- a/index.ipynb +++ b/index.ipynb @@ -10,13 +10,13 @@ }, "source": [ "---\n", - "title: Paired residue prediction dependencies in ESM2\n", + "title: \"{{< var pub.title >}}\"\n", "author:\n", " - name: Evan Kiefl\n", " orcid: 0000-0002-6473-0921\n", " corresponding: true\n", " email: evan.kiefl@arcadiascience.com\n", - "date: 'December 17, 2024'\n", + "date: 'January 1, 2025'\n", "reference-location: margin\n", "bibliography: ref.bib\n", "csl: assets/arcadia.csl\n", @@ -31,6 +31,35 @@ "source": [ "## Introduction\n", "\n", + "This is a template notebook that once edited by you, will become your publication.\n", + "\n", + "To see how a live preview of how the notebook renders into a publication, follow the instructions in the `README.md` (spoiler: `make preview`). And to view the published version of this template see [here](https://arcadia-science.github.io/notebook-pub-template/).\n", + "\n", + "## Getting started\n", + "\n", + "If you already have a notebook, replace this file with it. While a this will properly render (`make preview`)\n", + "\n", + "## Quarto Resources\n", + "\n", + "\n", + "\n", + "## Examples\n", + "\n", + "\n", + "\n", + "If you already have a notebook, you . Follow the instructions\n", + "\n", + "See the [README.md](https://github.com/Arcadia-Science/notebook-pub-template/blob/main/index.ipynb)\n", + "\n", + "The Arcadia template.\n", + "\n", + "[Quarto](https://quarto.org/) is a technical publishing system that can render Jupyter notebooks, R Markdown documents, and other file formats into stylistically rendered documents render for publication.\n", + "\n", + "\n", + "This short demo examples some of the features at your disposal. You can see how it's published here: [https://arcadia-science.github.io/notebook-pub-template/](https://arcadia-science.github.io/notebook-pub-template/).\n", + "\n", + "\n", + "\n", "This notebook details a quick analysis we performed on the ESM2 (Evolutionary Scale Modeling) model for masked token prediction. We stumbled upon a counter-intuitive result related to the effect that masking one residue has on the distribution of another.\n", "\n", "Before jumping into our results, let's first establish what masked token prediction is, how it works, and our consequent motivation for this analysis.\n",