Add About and TOC

_bookdown.yml

@@ -2,17 +2,23 @@ book_filename: "Course_Name"
 chapter_name: "Chapter "
 repo: https://github.com/jhudsl/AnVIL_Template/
 rmd_files: ["index.Rmd",
-            "01-intro.Rmd",
-            "02-chapter_of_course.Rmd",
-            "03-AnVIL_modules.Rmd",
-            "04-workspace_modules.Rmd",
-            "05-billing_modules.Rmd",
-            "06-onboarding_modules.Rmd",
-            "07-using_platforms_modules.Rmd",
-            "08-student_modules.Rmd",
-            "10-user_management_modules.Rmd",
-            "11-why-anvil.Rmd",
-            "12-instructor_modules.Rmd",
+            "organizer-guide.Rmd",
+            "scalable-ml.Rmd",
+            "prs-analysis.Rmd",
+            "variant-seqr.Rmd",
+            "biodigs-classroom.Rmd",
+            "wrap-tool.Rmd",
+            # "01-intro.Rmd",
+            # "02-chapter_of_course.Rmd",
+            # "03-AnVIL_modules.Rmd",
+            # "04-workspace_modules.Rmd",
+            # "05-billing_modules.Rmd",
+            # "06-onboarding_modules.Rmd",
+            # "07-using_platforms_modules.Rmd",
+            # "08-student_modules.Rmd",
+            # "10-user_management_modules.Rmd",
+            # "11-why-anvil.Rmd",
+            # "12-instructor_modules.Rmd",
             "About.Rmd",
             "References.Rmd"]
 new_session: yes

biodigs-classroom.Rmd

@@ -0,0 +1 @@
+# BioDIGS in the Classroom

index.Rmd

@@ -10,31 +10,27 @@ description: Description about Course/Book.
 favicon: assets/AnVIL_style/anvil_favicon.ico
 ---
 
+# What are CoFests!? {-}
 
-# About this Book {-}
+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.
 
-This book is part of a series of books for the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) of the National Human Genome Research Institute (NHGRI). Learn more about AnVIL by visiting https://anvilproject.org or reading the [article in Cell Genomics](https://www.sciencedirect.com/science/article/pii/S2666979X21001063).
+* *Modified from https://galaxyproject.org/events/cofests*
 
-## Skills Level {-} 
+## What's in a name: CollaborationFests! and Hackathons {- .unlisted}
 
-::: {.notice}
-_Genetics_
-<!-- **Novice**: no genetics knowledge needed -->
+We collaborate.
 
-_Programming skills_
-<!-- **Novice**: no programming experience needed -->
-:::
+AnVIL collaborative events are emphatically called CollaborationFests! rather than Hackathons.
+Putting **Collaboration** in the name emphasizes what the events are about for us, and **Fest** communicates that they are fun events (which they are).
 
-## AnVIL Collection {-}
+"Hackathon" implies an emphasis on code.
+CoFests! are about contributing and learning how to contribute to all aspects of AnVIL, including training material, community infrastructure, documentation, unit tests, bug reports, and yes, even code.
+First and foremost AnVIL CoFests! are about growing the community of future contributors.
 
-Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/
-
-# Learning Objectives {-}
+* *Idea inspiration from [[GCC2024](https://galaxyproject.org/events/gcc2024/cofest)][[GCC2018](https://galaxyproject.org/events/gccbosc2018/collaboration)]*
+* *Reporting inspiration from [[BioC2018](https://bioconductor.github.io/BiocWorkshops)][[BioC2020](http://bioc2020.bioconductor.org/workshops.html)][[BioC2023](https://bioc2023.bioconductor.org/workshops/)]*
 
-<!-- Learning objectives for this activity come from the [Genetics Core Competencies](https://genetics-gsa.org/education/genetics-learning-framework/): -->
+## AnVIL Collection {- .unlisted}
 
-<!-- - Objective 1 -->
-<!-- - Objective 2 -->
-<!-- - Objective 3 -->
-
-<!-- Please also see the Bioinformatics core competencies for undergraduate life sciences education from NIBLSE: https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0196878.t002 -->
+Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/

organizer-guide.Rmd

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+# Organizer Guide {-}
+
+The inaugural AnVIL Community Conference 2024 CoFests! will take place on November 12-13, 2024 in Cold Spring Harbor, NY.
+This event is a key event for professionals in the genomics community interested in biomedical and genomic cloud computing and takes place immediately before the sixth meeting on [Biological Data Science](https://meetings.cshl.edu/meetings.aspx?meet=DATA&year=24).
+
+- https://anvilproject.org/events/anvil2024-community-conference
+
+## CoFests! Goals {- .unlisted}
+
+- Build community
+- Develop high interest topics
+- Open science
+
+## Logistics {- .unlisted}
+
+- Parallel tracks, 5+ hours across Nov 12/13
+- Scientific Lead and Co-Lead
+- ~4-10 participants per topic
+
+## Example Schedule {- .unlisted}
+
+- Problem statement (short demo)
+- Brainstorming
+- Onboarding
+- Work-regroup, work-regroup
+- Report out

prs-analysis.Rmd

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+# Polygenic Risk Score Analysis

scalable-ml.Rmd

@@ -0,0 +1,3 @@
+# (PART\*) Topics {-}
+
+# Scalable ML and Data Science

variant-seqr.Rmd

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+# Variant Analysis with seqr

wrap-tool.Rmd

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+# Wrap a Tool with WDL