Merge branch 'main' into fillOutOrganizerGuide

.gitignore

@@ -8,3 +8,6 @@ spell_check_results.tsv
 .RData
 .httr-oauth
 docker/git_token.txt
+.Rproj.user
+.Rbuildignore
+*.Rproj

docs/404.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-17" />
+<meta name="date" content="2024-09-18" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -87,7 +87,10 @@
 
 <li class="divider"></li>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
-<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>

docs/About.md

@@ -53,7 +53,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-09-17
+##  date     2024-09-18
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────

docs/about-the-authors.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-17" />
+<meta name="date" content="2024-09-18" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -87,7 +87,10 @@
 
 <li class="divider"></li>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
-<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
@@ -272,7 +275,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-09-17
+##  date     2024-09-18
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────

docs/index.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-17" />
+<meta name="date" content="2024-09-18" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -87,7 +87,10 @@
 
 <li class="divider"></li>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
-<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
@@ -131,7 +134,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">AnVIL CoFests! 2024</h1>
-<p class="date"><em>September 17, 2024</em></p>
+<p class="date"><em>September 18, 2024</em></p>
 </div>
 <div id="what-are-cofests" class="section level1 unnumbered hasAnchor">
 <h1>What are CoFests!?<a href="index.html#what-are-cofests" class="anchor-section" aria-label="Anchor link to header"></a></h1>

docs/index.md

@@ -1,6 +1,6 @@
 ---
 title: "AnVIL CoFests! 2024"
-date: "September 17, 2024"
+date: "September 18, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: book.bib
@@ -15,7 +15,7 @@ favicon: assets/AnVIL_style/anvil_favicon.ico
 CollaborationFests!, also known as **CoFests!** (and sometimes as "hackathons"), are collaborative work events where we expand and improve the AnVIL community and the AnVIL ecosystem.
 Sometimes these gatherings are focused on AnVIL, and sometimes they are part of larger communities.
 
-* *Modified from https://galaxyproject.org/events/cofests*
+* *Modified from <https://galaxyproject.org/events/cofests>*
 
 ## What's in a name: CollaborationFests! and Hackathons {- .unlisted}
 

docs/organizer-guide.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-17" />
+<meta name="date" content="2024-09-18" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -87,7 +87,10 @@
 
 <li class="divider"></li>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
-<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
@@ -139,31 +142,105 @@ <h1>Organizer Guide<a href="organizer-guide.html#organizer-guide" class="anchor-
 <div id="cofests-goals" class="section level2 unnumbered unlisted hasAnchor">
 <h2>CoFests! Goals<a href="organizer-guide.html#cofests-goals" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <ul>
-<li>Build community</li>
-<li>Develop high interest topics</li>
-<li>Open science</li>
+<li>Build an inclusive community that is supportive of newcomers</li>
+<li>Contribute to <a href="https://en.wikipedia.org/wiki/Open_science">open science</a></li>
+<li>Produce a final product that accomplishes one of the following for a topic
+<ul>
+<li>Makes useful forward progress</li>
+<li>Identifies opportunities and boundaries or limitations</li>
+</ul></li>
 </ul>
 </div>
 <div id="logistics" class="section level2 unnumbered unlisted hasAnchor">
 <h2>Logistics<a href="organizer-guide.html#logistics" class="anchor-section" aria-label="Anchor link to header"></a></h2>
 <ul>
-<li>Parallel tracks, 5+ hours across Nov 12/13</li>
-<li>Scientific Lead and Co-Lead</li>
-<li>~4-10 participants per topic</li>
-</ul>
-</div>
-<div id="example-schedule" class="section level2 unnumbered unlisted hasAnchor">
-<h2>Example Schedule<a href="organizer-guide.html#example-schedule" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<li>3 Parallel tracks, 5+ hours across Nov 12/13
 <ul>
-<li>Problem statement (short demo)</li>
-<li>Brainstorming</li>
-<li>Onboarding</li>
-<li>Work-regroup, work-regroup</li>
-<li>Report out</li>
+<li>Scalable Machine Learning and Data Science</li>
+<li>Polygenic Risk Score Analysis</li>
+<li>Wrap a Tool (+ Intro AnVIL/WDL)</li>
+</ul></li>
+<li>Scientific Lead and AnVIL Outreach co-Lead for support</li>
+<li>We expect 4-10 participants per track</li>
 </ul>
+<p>Prior to the CoFests, the scientific and AnVIL Outreach co-Leads will work together to enumerate some ideas for final products and post them publicly in this book.</p>
+<div class="notice">
+<p>The AnVIL Outreach co-Lead will help add content to this guide, onboard newer AnVIL users to the platform, and provide guidance on the final product / report out.</p>
+</div>
+</div>
+<div id="final-product-report-out" class="section level2 unnumbered hasAnchor">
+<h2>Final Product / Report Out<a href="organizer-guide.html#final-product-report-out" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<p>The final product of CoFests doesn’t need to be code! These Collaboration Fests can support story-boarding future work or development of documentation or training materials. If it’s something that will help the community and make progress on an AnVIL associated topic and there’s sufficient interest, the idea is game! <a href="https://galaxyproject.org/events/gcc2023/cofest/#goals">As Galaxy phrased it for their CoFests:</a></p>
+<blockquote>
+<p>[The goal of collaboration fests is to expand the ecosystem] Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code.</p>
+</blockquote>
+<div class="notice">
+<p>It helps us a lot if you can fill out some basic <a href="https://docs.google.com/document/d/1wLK88p_tY6L-a8IF5dIe7gmDlJC1RxeU8_pm1ClU2IE/edit?usp=sharing">Report Out details</a>. At the end of Day 2, your track will <strong>share a final report during the CoFest Recap Session</strong>!</p>
+</div>
+</div>
+<div id="example-schedule-for-a-track" class="section level2 unnumbered unlisted hasAnchor">
+<h2>Example Schedule for a Track<a href="organizer-guide.html#example-schedule-for-a-track" class="anchor-section" aria-label="Anchor link to header"></a></h2>
+<div id="day-1-2.5-hours" class="section level3 unnumbered hasAnchor">
+<h3>Day 1 (2.5 hours)<a href="organizer-guide.html#day-1-2.5-hours" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<table>
+<colgroup>
+<col width="67%" />
+<col width="32%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="center">Task</th>
+<th align="center">Time &amp; Lead</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="center"><strong>Problem statement.</strong> Provide background info on the track’s overall topic and may include a brief summary of the pre-worked collaboration ideas.</td>
+<td align="center">20-30 minutes (Scientific Lead)</td>
+</tr>
+<tr class="even">
+<td align="center"><strong>Brainstorming.</strong> What project will the track tackle? Focus on understanding the participant backgrounds and skills and matching those with track ideas and actionable tasks to accomplish the goal.</td>
+<td align="center">15-30 minutes (Both)</td>
+</tr>
+<tr class="odd">
+<td align="center"><strong>Onboarding.</strong> Handle billing accounts and other logistics necessary to accomplish the work.</td>
+<td align="center">30-60 minutes (AnVIL Outreach co-Lead)</td>
+</tr>
+<tr class="even">
+<td align="center"><strong>Work-regroup, work-regroup.</strong> Formal collaboration work time left before dinner. (Groups may choose to work together informally after dinner too)</td>
+<td align="center">30-60 minutes (N/A)</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div id="day-2-3-hours" class="section level3 unnumbered hasAnchor">
+<h3>Day 2 (3 hours)<a href="organizer-guide.html#day-2-3-hours" class="anchor-section" aria-label="Anchor link to header"></a></h3>
+<table>
+<colgroup>
+<col width="67%" />
+<col width="32%" />
+</colgroup>
+<thead>
+<tr class="header">
+<th align="center">Task</th>
+<th align="left">Time &amp; Lead</th>
+</tr>
+</thead>
+<tbody>
+<tr class="odd">
+<td align="center"><strong>Work-regroup, work-regroup.</strong> Formal collaboration work time (with a coffee break).</td>
+<td align="left">2-2.5 hours (N/A)</td>
+</tr>
+<tr class="even">
+<td align="center"><strong>Construct a “report out”.</strong> The report out may be a Google doc, Google slides, a GitHub repository, <a href="https://github.com/jhudsl/OTTR_Template_Website">a website</a>, an <a href="https://github.com/jhudsl/OTTR_Template">OTTR book</a>, etc.</td>
+<td align="left">30-60 minutes (AnVIL Outreach co-Lead)</td>
+</tr>
+</tbody>
+</table>
 
 </div>
 </div>
+</div>
 
 
 

docs/organizer-guide.md

@@ -7,20 +7,51 @@ This event is a key event for professionals in the genomics community interested
 
 ## CoFests! Goals {- .unlisted}
 
-- Build community
-- Develop high interest topics
-- Open science
+- Build an inclusive community that is supportive of newcomers
+- Contribute to [open science](https://en.wikipedia.org/wiki/Open_science)
+- Produce a final product that accomplishes one of the following for a topic
+  - Makes useful forward progress
+  - Identifies opportunities and boundaries or limitations
 
 ## Logistics {- .unlisted}
 
-- Parallel tracks, 5+ hours across Nov 12/13
-- Scientific Lead and Co-Lead
-- ~4-10 participants per topic
+- 3 Parallel tracks, 5+ hours across Nov 12/13
+  - Scalable Machine Learning and Data Science
+  - Polygenic Risk Score Analysis
+  - Wrap a Tool (+ Intro AnVIL/WDL)
+- Scientific Lead and AnVIL Outreach co-Lead for support
+- We expect 4-10 participants per track
 
-## Example Schedule {- .unlisted}
+Prior to the CoFests, the scientific and AnVIL Outreach co-Leads will work together to enumerate some ideas for final products and post them publicly in this book.
 
-- Problem statement (short demo)
-- Brainstorming
-- Onboarding
-- Work-regroup, work-regroup
-- Report out
+::: {.notice}
+The AnVIL Outreach co-Lead will help add content to this guide, onboard newer AnVIL users to the platform, and provide guidance on the final product / report out.
+:::
+
+## Final Product / Report Out {-}
+
+The final product of CoFests doesn't need to be code! These Collaboration Fests can support story-boarding future work or development of documentation or training materials. If it's something that will help the community and make progress on an AnVIL associated topic and there's sufficient interest, the idea is game! [As Galaxy phrased it for their CoFests:](https://galaxyproject.org/events/gcc2023/cofest/#goals)
+
+> [The goal of collaboration fests is to expand the ecosystem] Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code.  
+
+::: {.notice}
+It helps us a lot if you can fill out some basic [Report Out details](https://docs.google.com/document/d/1wLK88p_tY6L-a8IF5dIe7gmDlJC1RxeU8_pm1ClU2IE/edit?usp=sharing). At the end of Day 2, your track will **share a final report during the CoFest Recap Session**!  
+:::
+
+## Example Schedule for a Track {- .unlisted}
+
+### Day 1 (2.5 hours) {-}
+
+| Task                      | Time & Lead |
+|:-------------------------:|:-----------:|
+| **Problem statement.** Provide background info on the track's overall topic and may include a brief summary of the pre-worked collaboration ideas. | 20-30 minutes (Scientific Lead) |
+| **Brainstorming.** What project will the track tackle? Focus on understanding the participant backgrounds and skills and matching those with track ideas and actionable tasks to accomplish the goal. | 15-30 minutes (Both) |
+| **Onboarding.** Handle billing accounts and other logistics necessary to accomplish the work. | 30-60 minutes (AnVIL Outreach co-Lead) | 
+| **Work-regroup, work-regroup.** Formal collaboration work time left before dinner. (Groups may choose to work together informally after dinner too) | 30-60 minutes (N/A) |
+
+### Day 2 (3 hours) {-}
+
+| Task                      | Time & Lead |
+|:-------------------------:|:------------|
+| **Work-regroup, work-regroup.** Formal collaboration work time (with a coffee break). | 2-2.5 hours (N/A) |
+| **Construct a "report out".** The report out may be a Google doc, Google slides, a GitHub repository, [a website](https://github.com/jhudsl/OTTR_Template_Website), an [OTTR book](https://github.com/jhudsl/OTTR_Template), etc. | 30-60 minutes (AnVIL Outreach co-Lead) |

docs/polygenic-risk-score-analysis.html

@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-17" />
+<meta name="date" content="2024-09-18" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -87,7 +87,10 @@
 
 <li class="divider"></li>
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
-<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>