From 754849a52ba4d85ab08b9111a3cec486e6638a4e Mon Sep 17 00:00:00 2001 From: Elizabeth Humphries Date: Thu, 7 Nov 2024 12:27:22 -0500 Subject: [PATCH 1/7] add prs workspace to prs chapter --- prs-analysis.Rmd | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/prs-analysis.Rmd b/prs-analysis.Rmd index dc74490..90190bb 100644 --- a/prs-analysis.Rmd +++ b/prs-analysis.Rmd @@ -4,12 +4,12 @@ Led by: Matthew Lebo, Harvard Medical School AnVIL Outreach coordinator: Elizabeth Humphries -About This Track - - +##Overview 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. + +## Workspace -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. \ No newline at end of file +The workspace for this track can be found at [https://anvil.terra.bio/#workspaces/mgb-lmm-clinical/AnVIL_CoFest2024_PRS_Analysis](https://anvil.terra.bio/#workspaces/mgb-lmm-clinical/AnVIL_CoFest2024_PRS_Analysis). This is a private workspace, so you will have to be given permission in order to view it. Participants in this tract should contact Elizabeth Humphries if they cannot access the workspace. \ No newline at end of file From 6a02687936a03a05fa1b34ce671ebbb463b2a246 Mon Sep 17 00:00:00 2001 From: Elizabeth Humphries Date: Thu, 7 Nov 2024 13:14:48 -0500 Subject: [PATCH 2/7] fix subheader in prs --- prs-analysis.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/prs-analysis.Rmd b/prs-analysis.Rmd index 90190bb..6a62637 100644 --- a/prs-analysis.Rmd +++ b/prs-analysis.Rmd @@ -4,7 +4,7 @@ Led by: Matthew Lebo, Harvard Medical School AnVIL Outreach coordinator: Elizabeth Humphries -##Overview +## About 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. From 40fffece040e2765ba0fd0f73a08198331b40fcf Mon Sep 17 00:00:00 2001 From: javibio-git Date: Fri, 8 Nov 2024 11:46:07 -0500 Subject: [PATCH 3/7] Added workspace and prep work to WDL --- wrap-tool.Rmd | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/wrap-tool.Rmd b/wrap-tool.Rmd index 4413c22..b4fcf0d 100644 --- a/wrap-tool.Rmd +++ b/wrap-tool.Rmd @@ -8,6 +8,17 @@ AnVIL Outreach coordinator: Javier Carpinteyro-Ponce 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. +## Workspace + +The workspace for this topic can be found at [https://anvil.terra.bio/#workspaces/acc2024-cofest-wdl/AnVIL_CoFest2024_Wrap-a-tool-in-WDL](https://anvil.terra.bio/#workspaces/acc2024-cofest-wdl/AnVIL_CoFest2024_Wrap-a-tool-in-WDL). + +## Prep work + +Participants on this topics should: + + 1. Download the Dockstore desktop app from [https://www.docker.com/products/docker-desktop/](https://www.docker.com/products/docker-desktop/). + 2. Register for a DockerHub account at [https://hub.docker.com/](https://hub.docker.com/). + ## Schedule ### Tuesday Nov 12, 2024 (2.5 hours) From 1882f418a4acbbdc55c87a47c34fe8db6f3fe3a8 Mon Sep 17 00:00:00 2001 From: Elizabeth Humphries Date: Fri, 8 Nov 2024 12:01:42 -0500 Subject: [PATCH 4/7] Update dictionary.txt --- resources/dictionary.txt | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/resources/dictionary.txt b/resources/dictionary.txt index 67f6373..ab67efc 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -1,3 +1,4 @@ +acc ACC Anshul AnVIL @@ -15,6 +16,7 @@ Callout Carpinteyro ChIP Cliffe +cofest CoFest cofests CoFests @@ -42,8 +44,10 @@ Jupyter Kundaje Lebo limma +lmm MDS mentorship +mgb NCI NHGRI NHGRI's @@ -68,9 +72,12 @@ RStudio Scalable seqr skillset +terra timeframe underserved Vivek +Vivekanandan +wdl WDL wip workspaces From 6a8e7ff444da81a01860d1ac1150d13348b90f46 Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 8 Nov 2024 14:24:02 -0500 Subject: [PATCH 5/7] workspace links for ml track --- scalable-ml.Rmd | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/scalable-ml.Rmd b/scalable-ml.Rmd index 3f64639..bdb8e3b 100644 --- a/scalable-ml.Rmd +++ b/scalable-ml.Rmd @@ -2,7 +2,7 @@ # Deploying, Training, and Interpreting Deep Learning Models for regulatory genomics in AnVIL -Led by: Anshul Kundaje & Vivek Ramalingam, Stanford University +Led by: Anshul Kundaje & Vivekanandan Ramalingam, Stanford University AnVIL Outreach coordinator: Kate Isaac @@ -10,6 +10,13 @@ AnVIL Outreach coordinator: Kate Isaac 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. +## Workspaces + +The workspaces that will be used for this CoFest! are used to train and analyze basepair resolution neural network models on Transcription factor ChIP-seq datasets (BPNet) and to process train and analyze ChromBPNet style models on ATAC and DNase datasets. + +- [BPNet workspace](https://anvil.terra.bio/#workspaces/terra-billing-vir/BPNet) +- [ChromBPNet workspace](https://anvil.terra.bio/#workspaces/terra-billing-vir/ChromBPNet) + ## 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. From a8c002887f50065986359d5fc9ffeb695b232f3c Mon Sep 17 00:00:00 2001 From: Kate Isaac <41767733+kweav@users.noreply.github.com> Date: Fri, 8 Nov 2024 14:30:12 -0500 Subject: [PATCH 6/7] address spell check --- resources/dictionary.txt | 3 +++ scalable-ml.Rmd | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/resources/dictionary.txt b/resources/dictionary.txt index ab67efc..9785574 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -11,10 +11,12 @@ bioinformatics biomedical BIPOC Bloomberg +BPNet callout Callout Carpinteyro ChIP +ChromBPNet Cliffe cofest CoFest @@ -26,6 +28,7 @@ CoV customizations dex dexamethasone +DNase dropdown galaxyproject GDSCN diff --git a/scalable-ml.Rmd b/scalable-ml.Rmd index bdb8e3b..6c5c28c 100644 --- a/scalable-ml.Rmd +++ b/scalable-ml.Rmd @@ -12,7 +12,7 @@ The "Deploying, Training, and Interpreting Deep Learning Models for Regulatory G ## Workspaces -The workspaces that will be used for this CoFest! are used to train and analyze basepair resolution neural network models on Transcription factor ChIP-seq datasets (BPNet) and to process train and analyze ChromBPNet style models on ATAC and DNase datasets. +The workspaces that will be used for this CoFest! are used to train and analyze base pair resolution neural network models on Transcription factor ChIP-seq datasets (BPNet) and to process train and analyze ChromBPNet style models on ATAC and DNase datasets. - [BPNet workspace](https://anvil.terra.bio/#workspaces/terra-billing-vir/BPNet) - [ChromBPNet workspace](https://anvil.terra.bio/#workspaces/terra-billing-vir/ChromBPNet) From 9264bcb8d4597e75aff890c82aecd830576cf1d9 Mon Sep 17 00:00:00 2001 From: Elizabeth Humphries Date: Fri, 8 Nov 2024 15:02:43 -0500 Subject: [PATCH 7/7] exclamation points were missing!!!!! --- prs-analysis.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/prs-analysis.Rmd b/prs-analysis.Rmd index 6a62637..8b3e2df 100644 --- a/prs-analysis.Rmd +++ b/prs-analysis.Rmd @@ -8,7 +8,7 @@ AnVIL Outreach coordinator: Elizabeth Humphries 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. +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. ## Workspace