diff --git a/prs-analysis.Rmd b/prs-analysis.Rmd index dc74490..8b3e2df 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 - - +## 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. - +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 diff --git a/resources/dictionary.txt b/resources/dictionary.txt index 67f6373..9785574 100644 --- a/resources/dictionary.txt +++ b/resources/dictionary.txt @@ -1,3 +1,4 @@ +acc ACC Anshul AnVIL @@ -10,11 +11,14 @@ bioinformatics biomedical BIPOC Bloomberg +BPNet callout Callout Carpinteyro ChIP +ChromBPNet Cliffe +cofest CoFest cofests CoFests @@ -24,6 +28,7 @@ CoV customizations dex dexamethasone +DNase dropdown galaxyproject GDSCN @@ -42,8 +47,10 @@ Jupyter Kundaje Lebo limma +lmm MDS mentorship +mgb NCI NHGRI NHGRI's @@ -68,9 +75,12 @@ RStudio Scalable seqr skillset +terra timeframe underserved Vivek +Vivekanandan +wdl WDL wip workspaces diff --git a/scalable-ml.Rmd b/scalable-ml.Rmd index 3604fbf..6c5c28c 100644 --- a/scalable-ml.Rmd +++ b/scalable-ml.Rmd @@ -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 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) + ## 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. 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)