diff --git a/_bookdown.yml b/_bookdown.yml index bae5ce5..e3e09bc 100644 --- a/_bookdown.yml +++ b/_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 diff --git a/biodigs-classroom.Rmd b/biodigs-classroom.Rmd new file mode 100644 index 0000000..e888613 --- /dev/null +++ b/biodigs-classroom.Rmd @@ -0,0 +1 @@ +# BioDIGS in the Classroom diff --git a/index.Rmd b/index.Rmd index 4b79e2a..1be86b2 100644 --- a/index.Rmd +++ b/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_ - +We collaborate. -_Programming skills_ - -::: +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/)]* - +## AnVIL Collection {- .unlisted} - - - - - +Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ diff --git a/organizer-guide.Rmd b/organizer-guide.Rmd new file mode 100644 index 0000000..6f5e8c4 --- /dev/null +++ b/organizer-guide.Rmd @@ -0,0 +1,26 @@ +# 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 diff --git a/prs-analysis.Rmd b/prs-analysis.Rmd new file mode 100644 index 0000000..29f700c --- /dev/null +++ b/prs-analysis.Rmd @@ -0,0 +1 @@ +# Polygenic Risk Score Analysis diff --git a/scalable-ml.Rmd b/scalable-ml.Rmd new file mode 100644 index 0000000..0c9a8dc --- /dev/null +++ b/scalable-ml.Rmd @@ -0,0 +1,3 @@ +# (PART\*) Topics {-} + +# Scalable ML and Data Science diff --git a/variant-seqr.Rmd b/variant-seqr.Rmd new file mode 100644 index 0000000..4467f24 --- /dev/null +++ b/variant-seqr.Rmd @@ -0,0 +1 @@ +# Variant Analysis with seqr diff --git a/wrap-tool.Rmd b/wrap-tool.Rmd new file mode 100644 index 0000000..d65db0c --- /dev/null +++ b/wrap-tool.Rmd @@ -0,0 +1 @@ +# Wrap a Tool with WDL