From 1ea0c04f7820cd88719c1e2328beb77101725195 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Thu, 7 Nov 2024 13:23:19 +0000 Subject: [PATCH] Render bookdown --- docs/404.html | 4 ++-- docs/About.md | 4 ++-- docs/about-the-authors.html | 8 ++++---- docs/brainstorming-feature-requests-for-anvil.html | 4 ++-- ...arning-models-for-regulatory-genomics-in-anvil.html | 4 ++-- docs/how-to-run-your-tool-in-anvil-with-wdl.html | 4 ++-- docs/index.html | 6 +++--- docs/index.md | 2 +- docs/organizer-guide.html | 4 ++-- docs/polygenic-risk-score-prs-analysis-in-anvil.html | 7 +++++-- docs/prs-analysis.md | 10 ++++++++++ docs/references.html | 4 ++-- docs/search_index.json | 2 +- 13 files changed, 38 insertions(+), 25 deletions(-) diff --git a/docs/404.html b/docs/404.html index 7819b03..5087590 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/About.md b/docs/About.md index 3344730..d530697 100644 --- a/docs/About.md +++ b/docs/About.md @@ -53,12 +53,12 @@ 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 2024-10-18 +## date 2024-11-07 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source -## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2) +## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html index 080b3dc..1bb1344 100644 --- a/docs/about-the-authors.html +++ b/docs/about-the-authors.html @@ -6,7 +6,7 @@ About the Authors | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + @@ -292,12 +292,12 @@

About the Authors Chapter 4 Brainstorming Feature Requests for AnVIL | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html b/docs/deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html index de286f4..73686bd 100644 --- a/docs/deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html +++ b/docs/deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html @@ -6,7 +6,7 @@ Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/how-to-run-your-tool-in-anvil-with-wdl.html b/docs/how-to-run-your-tool-in-anvil-with-wdl.html index cccc739..108b2bc 100644 --- a/docs/how-to-run-your-tool-in-anvil-with-wdl.html +++ b/docs/how-to-run-your-tool-in-anvil-with-wdl.html @@ -6,7 +6,7 @@ Chapter 3 How to Run Your Tool in AnVIL with WDL | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/index.html b/docs/index.html index 8bcff16..d472c8a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + @@ -151,7 +151,7 @@

What are CoFests!?

diff --git a/docs/index.md b/docs/index.md index 95cb3bf..30b4280 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,6 +1,6 @@ --- title: "AnVIL CoFests! 2024" -date: "October 18, 2024" +date: "November 07, 2024" site: bookdown::bookdown_site documentclass: book bibliography: book.bib diff --git a/docs/organizer-guide.html b/docs/organizer-guide.html index 0182bc1..9776c18 100644 --- a/docs/organizer-guide.html +++ b/docs/organizer-guide.html @@ -6,7 +6,7 @@ Organizer Guide | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/polygenic-risk-score-prs-analysis-in-anvil.html b/docs/polygenic-risk-score-prs-analysis-in-anvil.html index f005c45..f0be25d 100644 --- a/docs/polygenic-risk-score-prs-analysis-in-anvil.html +++ b/docs/polygenic-risk-score-prs-analysis-in-anvil.html @@ -6,7 +6,7 @@ Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + @@ -153,6 +153,9 @@

Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL

Led by: Matthew Lebo, Harvard Medical School

AnVIL Outreach coordinator: Elizabeth Humphries

+

About This Track

+

This track, run by the AnVIL Clinical Resource team, will consist of both an overview and a hands-on workshop to provide individuals with an understanding of polygenic scores and how to run and evaluate them in AnVIL. First, we will level-set by providing an overview of the current state of polygenic analysis, with a focus on polygenic risk scores (PRS). Next, we will jointly work with participants to run PRS analyses in AnVIL using the WDL framework. These tasks will increase in complexity in terms of analytical components of the workflow, with the goal of enabling users to run the WDL on their own. We will also engage with participants to get feedback and create user-friendly documents to enable processing of this workflow once published to the broader community. Finally, we will work with more advanced users to generate a new WDL focused on the evaluation of PRS among a cohort of individuals.

+

Participants are not required to supply their own data, as publicly available data and an AnVIL workspace will be provided as part of the CoFest track. Users who are interested in running the analyses on their own data are welcome, but should have their own workspace in which to run the analyses.

diff --git a/docs/prs-analysis.md b/docs/prs-analysis.md index ba18712..467466d 100644 --- a/docs/prs-analysis.md +++ b/docs/prs-analysis.md @@ -3,3 +3,13 @@ Led by: Matthew Lebo, Harvard Medical School AnVIL Outreach coordinator: Elizabeth Humphries + +About This Track + + + +This track, run by the AnVIL Clinical Resource team, will consist of both an overview and a hands-on workshop to provide individuals with an understanding of polygenic scores and how to run and evaluate them in AnVIL. First, we will level-set by providing an overview of the current state of polygenic analysis, with a focus on polygenic risk scores (PRS). Next, we will jointly work with participants to run PRS analyses in AnVIL using the WDL framework. These tasks will increase in complexity in terms of analytical components of the workflow, with the goal of enabling users to run the WDL on their own. We will also engage with participants to get feedback and create user-friendly documents to enable processing of this workflow once published to the broader community. Finally, we will work with more advanced users to generate a new WDL focused on the evaluation of PRS among a cohort of individuals. + + + +Participants are not required to supply their own data, as publicly available data and an AnVIL workspace will be provided as part of the CoFest track. Users who are interested in running the analyses on their own data are welcome, but should have their own workspace in which to run the analyses. diff --git a/docs/references.html b/docs/references.html index d575769..d9ba15f 100644 --- a/docs/references.html +++ b/docs/references.html @@ -6,7 +6,7 @@ Chapter 5 References | AnVIL CoFests! 2024 - + @@ -22,7 +22,7 @@ - + diff --git a/docs/search_index.json b/docs/search_index.json index 0f014c1..96591a2 100644 --- a/docs/search_index.json +++ b/docs/search_index.json @@ -1 +1 @@ -[["index.html", "AnVIL CoFests! 2024 What are CoFests!? What’s in a name: CollaborationFests! and Hackathons AnVIL Collection", " AnVIL CoFests! 2024 October 18, 2024 What are CoFests!? 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 What’s in a name: CollaborationFests! and Hackathons We collaborate. 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). “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. Idea inspiration from [GCC2024][GCC2018] Reporting inspiration from [BioC2018][BioC2020][BioC2023] AnVIL Collection Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["organizer-guide.html", "Organizer Guide CoFests! Goals Logistics Final Product / Report Out Example Schedule for a Track", " Organizer Guide The inaugural AnVIL Community Conference (ACC) 2024 will take place on November 12-13, 2024 in Cold Spring Harbor, NY, immediately before the sixth meeting on Biological Data Science. Overall, ACC is a key event for professionals in the genomics community interested in biomedical and genomic cloud computing and features keynotes, town halls, CoFests! and other such component events. CoFests! provide attendees the opportunity to get some hands-on experience with AnVIL and foster connections within the AnVIL community. CoFests! Goals Build an inclusive community that is supportive of newcomers Collaborate and contribute to 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 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 coordinator for support We expect 4-10 participants per track Prior to the CoFests, the scientific lead and AnVIL Outreach coordinators will work together to enumerate some ideas for final products and post them publicly in this book. The AnVIL Outreach coordinator 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: [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. It helps us a lot if you can fill out some basic Report Out details. At the end of Day 2, your track will share a final report during the CoFest Recap Session! Example Schedule for a Track 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 coordinator) 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, an OTTR book, etc. 30-60 minutes (AnVIL Outreach coordinator) "],["deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html", "Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL 1.1 About This Track 1.2 Report Out", " Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL Led by: Anshul Kundaje & Vivek Ramalingam, Stanford University AnVIL Outreach coordinator: Kate Isaac 1.1 About This Track The “Deploying, Training, and Interpreting Deep Learning Models for Regulatory Genomics in AnVIL” CoFests! track at the AnVIL Community Conference offers hands-on training for users and developers interested in applying deep learning to regulatory genomics. This track aims to demonstrate how deep learning models can be utilized for functional genomics datasets, such as ChIP-seq and ATAC-seq, at scale via AnVIL. Participants will develop a comprehensive understanding of the steps involved in deploying, training, and interpreting these models, including the available input options and how to leverage the resulting outputs to address various biological questions. 1.2 Report Out At the conclusion of the CoFest!, we will spend some time to collaboratively develop a user guide for utilizing these deep learning workspaces. This user guide will be published on GitHub. "],["polygenic-risk-score-prs-analysis-in-anvil.html", "Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL", " Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL Led by: Matthew Lebo, Harvard Medical School AnVIL Outreach coordinator: Elizabeth Humphries "],["how-to-run-your-tool-in-anvil-with-wdl.html", "Chapter 3 How to Run Your Tool in AnVIL with WDL 3.1 About 3.2 Schedule", " Chapter 3 How to Run Your Tool in AnVIL with WDL Led by: Allie Cliffe, Broad Institute of MIT and Harvard AnVIL Outreach coordinator: Javier Carpinteyro-Ponce 3.1 About Workflow Description Language (WDL) not in your programming skillset? No problem! Learn to wrap your pipelining tool in WDL and run it in an AnVIL workspace in this CoFest! session. We’ll go over WDL basics and how to run pipelines in AnVIL, then walk through how to run your own Unix/Python/R script. Along the way, you’ll write a WDL and build a custom Docker to run it with. Come and wrap a tool of interest! All experience levels are welcome. We’ll brainstorm and, if time allows, we’ll create resources (tutorials? AnVIL book? Cheat sheet?) for others to use to run their non-WDL tool in AnVIL. 3.2 Schedule 3.2.1 Tuesday Nov 12, 2024 (2.5 hours) Task Time Pipelining in AnVIL + WDLs presentation 2:15pm - 3:00pm Running a WDL and running Python script wrapped in WDL 3:00pm - 4:00pm Brainstorming AnVIL resources for wrapping other tools in WDL 4:00pm - 4:45pm 3.2.2 Wednesday Nov 13, 2024 (3 hours) Task Time Hackathon-like effort to develop ideas from brainstorming 1:00pm - 2:30pm Coffee break 2:30pm - 3:00pm Report Out 3:00pm - 4:00pm CoFest! recap 4:00pm "],["brainstorming-feature-requests-for-anvil.html", "Chapter 4 Brainstorming Feature Requests for AnVIL 4.1 About This Track 4.2 Report Out", " Chapter 4 Brainstorming Feature Requests for AnVIL Led by: Ava Hoffman, Fred Hutch Cancer Center / AnVIL Outreach 4.1 About This Track The “Brainstorming Feature Requests” CoFest track at the AnVIL Community Conference provides an opportunity for users and developers to directly communicate their needs to the AnVIL Outreach Team. Participants can share their experiences with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL), highlighting both its strengths and areas for improvement. The AnVIL Outreach team will facilitate discussion, gaining insights into real-world use cases and challenges. This open dialogue will help identify gaps in functionality and potential enhancements that could significantly improve the platform’s utility for genomic researchers. 4.2 Report Out By the end of the CoFest, the team will have compiled a Report Out list of feature requests based on user feedback, ensuring that future development efforts are aligned with the community’s needs. This collaborative approach will shape AnVIL’s future and strengthen connections between AnVIL developers and community members. "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter AnVIL instructions: Katherine Cox, Ava Hoffman, Elizabeth Humphries Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content AnVIL instructions: Allie Cliffe Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-10-18 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.40 2024-07-02 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["references.html", "Chapter 5 References", " Chapter 5 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]] +[["index.html", "AnVIL CoFests! 2024 What are CoFests!? What’s in a name: CollaborationFests! and Hackathons AnVIL Collection", " AnVIL CoFests! 2024 November 07, 2024 What are CoFests!? 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 What’s in a name: CollaborationFests! and Hackathons We collaborate. 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). “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. Idea inspiration from [GCC2024][GCC2018] Reporting inspiration from [BioC2018][BioC2020][BioC2023] AnVIL Collection Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["organizer-guide.html", "Organizer Guide CoFests! Goals Logistics Final Product / Report Out Example Schedule for a Track", " Organizer Guide The inaugural AnVIL Community Conference (ACC) 2024 will take place on November 12-13, 2024 in Cold Spring Harbor, NY, immediately before the sixth meeting on Biological Data Science. Overall, ACC is a key event for professionals in the genomics community interested in biomedical and genomic cloud computing and features keynotes, town halls, CoFests! and other such component events. CoFests! provide attendees the opportunity to get some hands-on experience with AnVIL and foster connections within the AnVIL community. CoFests! Goals Build an inclusive community that is supportive of newcomers Collaborate and contribute to 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 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 coordinator for support We expect 4-10 participants per track Prior to the CoFests, the scientific lead and AnVIL Outreach coordinators will work together to enumerate some ideas for final products and post them publicly in this book. The AnVIL Outreach coordinator 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: [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. It helps us a lot if you can fill out some basic Report Out details. At the end of Day 2, your track will share a final report during the CoFest Recap Session! Example Schedule for a Track 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 coordinator) 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, an OTTR book, etc. 30-60 minutes (AnVIL Outreach coordinator) "],["deploying-training-and-interpreting-deep-learning-models-for-regulatory-genomics-in-anvil.html", "Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL 1.1 About This Track 1.2 Report Out", " Chapter 1 Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL Led by: Anshul Kundaje & Vivek Ramalingam, Stanford University AnVIL Outreach coordinator: Kate Isaac 1.1 About This Track The “Deploying, Training, and Interpreting Deep Learning Models for Regulatory Genomics in AnVIL” CoFests! track at the AnVIL Community Conference offers hands-on training for users and developers interested in applying deep learning to regulatory genomics. This track aims to demonstrate how deep learning models can be utilized for functional genomics datasets, such as ChIP-seq and ATAC-seq, at scale via AnVIL. Participants will develop a comprehensive understanding of the steps involved in deploying, training, and interpreting these models, including the available input options and how to leverage the resulting outputs to address various biological questions. 1.2 Report Out At the conclusion of the CoFest!, we will spend some time to collaboratively develop a user guide for utilizing these deep learning workspaces. This user guide will be published on GitHub. "],["polygenic-risk-score-prs-analysis-in-anvil.html", "Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL", " Chapter 2 Polygenic Risk Score (PRS) Analysis in AnVIL Led by: Matthew Lebo, Harvard Medical School AnVIL Outreach coordinator: Elizabeth Humphries About This Track This track, run by the AnVIL Clinical Resource team, will consist of both an overview and a hands-on workshop to provide individuals with an understanding of polygenic scores and how to run and evaluate them in AnVIL. First, we will level-set by providing an overview of the current state of polygenic analysis, with a focus on polygenic risk scores (PRS). Next, we will jointly work with participants to run PRS analyses in AnVIL using the WDL framework. These tasks will increase in complexity in terms of analytical components of the workflow, with the goal of enabling users to run the WDL on their own. We will also engage with participants to get feedback and create user-friendly documents to enable processing of this workflow once published to the broader community. Finally, we will work with more advanced users to generate a new WDL focused on the evaluation of PRS among a cohort of individuals. Participants are not required to supply their own data, as publicly available data and an AnVIL workspace will be provided as part of the CoFest track. Users who are interested in running the analyses on their own data are welcome, but should have their own workspace in which to run the analyses. "],["how-to-run-your-tool-in-anvil-with-wdl.html", "Chapter 3 How to Run Your Tool in AnVIL with WDL 3.1 About 3.2 Schedule", " Chapter 3 How to Run Your Tool in AnVIL with WDL Led by: Allie Cliffe, Broad Institute of MIT and Harvard AnVIL Outreach coordinator: Javier Carpinteyro-Ponce 3.1 About Workflow Description Language (WDL) not in your programming skillset? No problem! Learn to wrap your pipelining tool in WDL and run it in an AnVIL workspace in this CoFest! session. We’ll go over WDL basics and how to run pipelines in AnVIL, then walk through how to run your own Unix/Python/R script. Along the way, you’ll write a WDL and build a custom Docker to run it with. Come and wrap a tool of interest! All experience levels are welcome. We’ll brainstorm and, if time allows, we’ll create resources (tutorials? AnVIL book? Cheat sheet?) for others to use to run their non-WDL tool in AnVIL. 3.2 Schedule 3.2.1 Tuesday Nov 12, 2024 (2.5 hours) Task Time Pipelining in AnVIL + WDLs presentation 2:15pm - 3:00pm Running a WDL and running Python script wrapped in WDL 3:00pm - 4:00pm Brainstorming AnVIL resources for wrapping other tools in WDL 4:00pm - 4:45pm 3.2.2 Wednesday Nov 13, 2024 (3 hours) Task Time Hackathon-like effort to develop ideas from brainstorming 1:00pm - 2:30pm Coffee break 2:30pm - 3:00pm Report Out 3:00pm - 4:00pm CoFest! recap 4:00pm "],["brainstorming-feature-requests-for-anvil.html", "Chapter 4 Brainstorming Feature Requests for AnVIL 4.1 About This Track 4.2 Report Out", " Chapter 4 Brainstorming Feature Requests for AnVIL Led by: Ava Hoffman, Fred Hutch Cancer Center / AnVIL Outreach 4.1 About This Track The “Brainstorming Feature Requests” CoFest track at the AnVIL Community Conference provides an opportunity for users and developers to directly communicate their needs to the AnVIL Outreach Team. Participants can share their experiences with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL), highlighting both its strengths and areas for improvement. The AnVIL Outreach team will facilitate discussion, gaining insights into real-world use cases and challenges. This open dialogue will help identify gaps in functionality and potential enhancements that could significantly improve the platform’s utility for genomic researchers. 4.2 Report Out By the end of the CoFest, the team will have compiled a Report Out list of feature requests based on user feedback, ensuring that future development efforts are aligned with the community’s needs. This collaborative approach will shape AnVIL’s future and strengthen connections between AnVIL developers and community members. "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter AnVIL instructions: Katherine Cox, Ava Hoffman, Elizabeth Humphries Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content AnVIL instructions: Allie Cliffe Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-11-07 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.41 2024-10-16 [1] CRAN (R 4.3.2) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.48 2024-07-07 [1] CRAN (R 4.3.2) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.25 2023-09-18 [1] RSPM (R 4.3.0) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.48 2024-10-03 [1] CRAN (R 4.3.2) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["references.html", "Chapter 5 References", " Chapter 5 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]