Introducing AnVIL Demos! Starting March 23, 2023

AnVIL Demos
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Introducing AnVIL Demos!

:pencil: Sign up: https://forms.gle/7CcaLE9AM7FrYqpP7

What are AnVIL Demos?

Join us to see a highlight of what you can do on the NHGRI Analysis, Visualization, and Informatics Lab-space (AnVIL), a cloud-based computing platform for genomic data science! AnVIL Demos will start out with a 30-minute demonstration on the platform followed by open time for Q&A and user support.

The demos will highlight a range of topics, from a capability of the platform to a scientific analysis powered by AnVIL. If you’re interested in showcasing how you use AnVIL at a future AnVIL Demos session, reach out to Natalie Kucher (nkucher3@jhu.edu).

After the demo, we’ll open up the floor to answer questions about the demo and to answer any general questions you might have about AnVIL.

:play_or_pause_button: Watch our past Demos from our YouTube playlist!

March Demo: Introduction to AnVIL

March 23, 2023 at 11:00 AM ET (your timezone) on Zoom

11:00 AM - 11:30 AM ET – Demo on AnVIL

Stephen Mosher will kick off our first AnVIL Demo, showing off how to sign up for AnVIL and take a tour of the major platform components.

11:30 AM - 12:00 PM ET – Q&A

We’ll open up the floor to questions about the demo presented, and will have AnVIL and Terra support on call to answer any questions about AnVIL you might have!

:pencil:Sign up: https://forms.gle/7CcaLE9AM7FrYqpP7

Upcoming Demos

April 27, 2023 – Using the Human Pangenome on AnVIL

May 18, 2023 – WARP Pipelines in AnVIL/Terra

June 22, 2023 – How to use data across multiple AnVIL workspaces

Resources

Upcoming Events

Learn about the upcoming AnVIL events at AnVIL Community Events - AnVIL Portal!

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Q: Working with WES sequencing datasets, have a collaboration with Azure Cloud. AnVIL is in the process of migrating, what is the progress of this transition?

A: There is a limited trial version to use AnVIL on Azure, there is some limited support for notebooks on Azure, though not yet RStudio, Galaxy, or Workflows.

There is a limited-access preview to AnVIL on Azure that can be requested here: Introducing Terra on Azure - Terra.Bio.

Q: In theory, once the datasets are stored in Azure, they would be able to access the data in AnVIL? There are clinical records in the datasets, and need to be EHR approved. AnVIL would be a nice workbench to use for the data, and would be great to use. There will be bam files. Can contact the AnVIL group to migrate?

A: Controlled access to genomic data works today with GCP. Using patient data is not supported right now, and for many institutions Azure is HIPAA certified and will allow fuller support for accessing more protected datasets. Many datasets supported by NHGRI and NIH Cloud Platform Interoperability Project (NCPI) are available today.

Q: All of Us is using AnVIL, will other groups be using it as well?

A: All of Us uses the Researcher Workbench which is isolated from AnVIL. Terra underpins both of these efforts, but right now the data are currently siloed. There was a recent call for expanding AnVIL’s clinical offerings in the call for the AnVIL Clinical Resource (ACR) which will come online in the future. Many large consortia are using AnVIL today including eMERGE, GTEx, PRIMED, GREGoR, CCDG and CMGs.

Q: How feature compatible is All of Us to AnVIL? Does All of Us have workflows and Galaxy available?

A: It is primarily Jupyter and RStudio. You can spin up your own cromwell workflow engine on a single VM from a cloud environment. The execution of the workflow spins up new VMs for each task/shard just as they normally would when executing via AnVIL centralized Cromwell.