Terra on Microsoft Azure cloud computing continues to evolve to meet the demand for high-performance virtual machines (VMs) capable of handling intensive workloads. We’re thrilled to announce the availability of NCSv3 (NC6s_v3 and NC12s_v3) series GPU VMs, which bring unprecedented computational power to Terra, making it ideal for a wide range of applications such as Artificial Intelligence (AI), Machine Learning (ML), and Deep Learning (DL) for biomedical analysis.

Harnassing the power of NCSv3-series GPU VMs

NCSv3-series GPU VMs provide an exceptional level of performance by leveraging NVIDIA’s advanced GPU technology. You can take advantage of these updated GPUs powered by NVIDIA Tesla V100 GPUs on Terra for traditional High Performance Computing (HPC) workloads such as reservoir modeling, DNA sequencing, protein analysis, Monte Carlo simulations, and others. Working in Terra lets you easily access several datasets in the cloud such as Microsoft Genomics Data Lake without having to compete for fixed HPC resources. In addition to GPUs, the NCv3-series VMs are also powered by Intel Xeon E5-2690 v4 (Broadwell) CPUs. [Ref]

Accelerate model training and inferencing

Whether training neural networks or deploying real-time inferencing solutions, these virtual machines accelerate model training and inferencing tasks on Terra. With the NCSv3-series GPUs, you can bring your ML/DL models to real-life problems faster, empowering breakthroughs in biomedical research. 

A new era of High-Performance Computing (in the cloud)

The availability of NCSv3-series GPU VMs on Terra on Microsoft Azure brings a new era of high-performance computing to the biomedical computing landscape. With their exceptional GPU capabilities and extensive memory, these virtual machines let you tackle the most demanding workloads – from AI and ML to deep learning – all within the ecosystem of Terra on Microsoft Azure.

Try it out in a Microsoft Azure Public Workspace 

To get started, try our featured workspace, which includes a sample notebook for training the deep learning models. As of July 2023, running this notebook on the NC6s_v3 GPU VM in your own Terra on Microsoft Azure workspace costs about $3.06 per hour with the included data.Please use Microsoft Azure Pricing calculator for the latest price information. 

Important Note: Be sure to check GPU quotas from the Azure portal before deploying the GPU VMs on Terra on Microsoft Azure. Please check the Terra Support Article for step-by-step instructions as well as caveats and troubleshooting about quota increase requests.

View quotas – Azure Quotas | Microsoft Learn

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Interactive Genomic Viewer: Overview

The Interactive Genomic Viewer (IGV) is a powerful and popular visualization tool for exploring genomic data. It supports a range of genomic data types including aligned sequence reads, mutations, gene expression and genomic annotations. With IGV, you can zoom and explore genomic data at levels of detail ranging from whole genome to base pair. IGV supports data loaded from multiple sources ranging from cloud-based to local resources. To learn more about IGV, please refer to Robinson, J., Thorvaldsdóttir, H., Winckler, W. et al. Integrative genomics viewer. Nat Biotechnol 29, 24–26 (2011). https://doi.org/10.1038/nbt.1754.

How to use IGV in Terra on Azure

You can use IGV in Terra on Azure by running a Jupyter notebook. Jupyter notebooks are a great tool for data scientists working on genomic data analysis.

To learn more, see the IGV in Terra on Azure Featured Workspace. The Featured Workspace demonstrates the basics of using JupyterLab and IGV on Terra on Microsoft Azure with data from the Microsoft Genomics Data Lake.

For step-by-step instructions, see How to run IGV in a notebook in Terra Support. 

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VS Code is designed to let you seamlessly leverage the environments that make you most productive. You can work in the Windows Subsystem for Linux (WSL), remote machines via SSH, and dev containers directly from VS Code with the VS Code Remote Development extensions. These extensions install a server on the remote environment, allowing local VS Code to smoothly interact with remote source code and runtimes.

VS Code key features

VS Code comes with a host of features that make it a great choice for developers. 

• Intuitive interface: VS Code has a clean and intuitive interface that is easy to navigate.
• Integrated terminal: An integrated terminal allows developers to execute commands and run scripts without leaving the editor.
• Debugging: Built-in debugging support for a variety of languages makes it easy to debug code directly within the editor.
• Git integration: Manage source control from within the editor.
• Extensions: One advantage of using Visual Studio Code for genomics analysis is its extensive library of extensions to enhance its functionality and add new features for a wide range of languages and frameworks. Some popular extensions for genomics analysis provide syntax highlighting and autocompletion for the Python, R, and Julia programming languages.

VS Code Server

The Visual Studio Code Server (VS Code Server) is a service you can run on a remote development machine, like your desktop PC or a virtual machine (VM). It lets you securely connect to that remote machine from anywhere through a local VS Code client, without an SSH requirement (reference).

 The service is built on the underlying server used by the remote extensions and includes some additional functionality, like an interactive CLI and facilitating secure connections to vscode.dev ( reference).

VS Code Server benefits

• Remote Development: With VS Code server, you can develop code on a remote machine, allowing you to use your local machine for other tasks.
• Collaboration: VS Code server allows multiple developers to work on the same codebase/
• Cloud: VS Code server integrates with Microsoft Azure, allowing you to develop and deploy applications in the cloud.
• Secure: VS Code server uses SSH encryption, providing a secure connection between your Terra virtual environment and the remote server.

Access the New Featured Workspace 

Start the VS Code server from your Terra cloud environment and leverage the power of a Terra Microsoft Azure Data Science VM for the VS Code implementations with this featured workspace.

The post Boost your genomics analysis with VS Code Server on Terra on Microsoft Azure appeared first on Terra.

Since we introduced the new Analyses tab as an updated interface for creating and launching Cloud Environments (on an opt-in basis), we’ve received a lot of great feedback from the many members of the Terra community who have signed up to use it. That feedback is helping us further improve the interface, which is an important component of the work we are doing to better serve the research needs and preferences we are hearing from the community. 

In that spirit, I wanted to give you more visibility into our plans for making it possible to run a wider variety of analysis applications in Terra, in addition to the current lineup of Jupyter Notebook, RStudio and Galaxy.

Expanding the selection of integrated apps

As my colleague Sara Salahi previously touched on when she described her vision for supporting more workflow languages, we have been developing a new model for serving applications through Terra’s Cloud Environments system. Sara’s blog mentioned the prospect of running single-tenant instances of the Cromwell workflow manager, and of other workflow managers that will be added subsequently. (Don’t forget to vote in the Feature Requests section if you want us to prioritize CWL support, Nextflow support or something else!) 

We’re also planning to use that same system to integrate other third-party applications like the UCSC Genome Browser, which needs no introduction, and the Hail Batch Service, which facilitates running analyses based on the Hail genetics framework at large scale. 

Once those initial integrations are live, we plan to continue adding more applications to the platform based on the needs of the communities we support, which includes large consortia such as AnVIL and of course, the many individual researchers and labs who use Terra independently. If there is an application you would like to use in Terra, please post a Feature Request, or upvote the relevant request if what you want has already been suggested.  

Official integration or “bring-your-own-app”?

For applications with a wide appeal, we aim to collaborate with third-party developers to produce a containerized version of their application that can be made available to everyone through Terra as an “official” app. 

For other applications, we are considering a template-based system that would empower individual developers — including computational biologists and bioinformaticians who are comfortable with a certain level of coding— to produce their own “custom” app and run it within their own environments. We are very interested in hearing from people who would want to use such a capability; if that’s you, please upvote the “bring-your-own-app” feature request in the forum, and/or reach out to the support team if you’re willing to provide detailed input on this question.

We look forward to rolling out the first of these new app integrations later this year, and in the meantime, we hope to hear from you so we can adjust our plans to best suit your needs!

The post Terra’s roadmap to supporting more analysis applications appeared first on Terra.

As increasing amounts of biomedical research data moves to the cloud, our goal is to provide you with the tools you need to perform all of the relevant analyses in one place. Accordingly, we’ve been working to adapt Terra’s Cloud Environments system to support a wider range of interactive analysis applications. This is a multi-step process that we’ll be talking about in several upcoming blog posts; today I’m excited to unveil the first step on this journey, which we’re inviting you to take with us. 

We’ve been redesigning the part of the interface that provides access to the interactive analysis applications supported by Cloud Environments, i.e. Jupyter Notebook, RStudio and Galaxy. The new design aims to provide a more consistent and intuitive experience across these applications as well as those we plan to add in the future. 

To ensure we’re heading in the right direction, we’re releasing the new design as an opt-in beta version and inviting you to give us feedback on how it’s looking so far. 

Highlights of the new design

Under the new design, the “Notebooks” tab is transformed into the more general “Analyses” tab, from where you can access the multiple applications available for Interactive Analysis in Terra. Accordingly, the list of Notebook files (.ipynb) becomes the list of “Your Analyses”, which now supports including R Markdown files (.Rmd). Just like Notebook files, any R Markdown files created in or added to the Analyses tab will be automatically stored in the workspace bucket and synced between the bucket and your persistent disk.

Finally, the Cloud Environment widget located at the top right-hand corner of the page moves to a new sidebar within the tab itself, where two buttons provide quick access to the Environment Configuration menu and the Terminal, respectively.

If you already have analysis files and a Cloud Environment set up, getting back to work is as easy as clicking on one of the files and following the prompts to open it in the relevant application.

Otherwise, click the Start button to create a new file or upload an existing file from your computer. If you don’t already have a suitable Cloud Environment set up, the system will walk you through the necessary steps to create one. 

A clearer path to configuring and managing your Cloud Environments

Previously, the environment configuration menu lived in the widget labeled Cloud Environment located at the top right-hand corner of the page. As noted above, we moved this functionality to a new sidebar in the Analyses tab, represented by a cloud icon, and officially renamed it “Environment Configuration”.

Clicking on the “Environment Configuration” icon opens the “Cloud Environment Details” pane shown below, which you can use to configure, start, stop, or edit your Cloud Environments.

As you can see in the screenshot, the Cloud Environment Details pane currently shows all three applications — Jupyter, RStudio, and Galaxy — as independent options. Be aware that Jupyter and RStudio are mutually exclusive, i.e. you can’t run both at the same time due to a current limitation of the system (to be addressed in future work). However, Galaxy can be run in parallel to either one of the other two.

When you start a Cloud Environment, the corresponding application logo (Jupyter, RStudio or Galaxy) appears in the sidebar of the Analyses tab, along with a colored dot that represents the status of that environment. You can view a more detailed visual and textual description of the environment’s status by clicking the Environment Configuration button (cloud icon) on the sidebar to display the Cloud Environment Details pane.

If you navigate away from your environment, you can always hop back in by clicking the corresponding logo in the sidebar.

To learn more about interactive analyses and Cloud Environments in Terra, see the Interactive Analysis section of the Terra support site. For step-by-step instructions on how to create a new interactive analysis environment for a specific application, see the relevant docs for Jupyter, RStudio and Galaxy.

Try it out and tell us what you think

You can activate the new design by going to the Notebooks tab in any workspace and clicking “Try new layout”. If at any point you decide you’d rather go back to the original design, simply click the “Revert layout” button. In either case, we’d be grateful if you could tell us what you think of the new version; every bit of feedback, be it positive or negative, will help us refine the design and ensure a more productive experience for everyone when we eventually switch to the new version.

The simplest way to send us your comments is to click on “Submit feedback” at the top of the Analyses tab, which will open a short survey (just 3 questions). You’re also welcome to reach out to the Helpdesk at any time, or comment in the community forum.

Resources

For more general information about Terra’s interactive analysis capabilities, see the following course and tutorials:

• Intro to Cloud Environments Leanpub course
• Notebooks Quickstart Guide

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