Merge pull request #24 from jhudsl/add-workspaces

Add workspaces for each track

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.
+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.

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

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.

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)