Clinical variant analysis experts with fully integrated workflows are often hesitant to upgrade or migrate their workspace, and rightly so. Similarly, those looking for new next-generation sequencing analysis software, whether for secondary (alignment and variant-calling) or tertiary (variant annotation, filtration, interpretation, and reporting) analysis, can be easily daunted by the breadth and depth of the process of setting up a new pipeline. In both cases, labs must wrangle infrastructure deployment or upgrades, the validation process, and the integration of existing systems. Thankfully, the flexibility and integration tools built into VSWarehouse 3 (VSW3) provide users with an environment that facilitates a seamless transition to an improved workspace.
The Story So Far
At Golden Helix, we’ve recently highlighted our efforts across our blogs and webcasts. Since introducing VS3’s cloud capabilities in an excellent webcast by Gabe Rudy, our Vice President of Product and Engineering, we’ve expounded upon VSW3’s native automation capabilities in a webcast presented by myself and Darby Kammeraad, our Director of Customer Success. We also shared more details on bridging the gap between cloud and on-premise during our most recent webcast from Gabe Rudy.
Our development team has also chimed in with some great resources. Dr. Nathan Fortier, our Director of Research, shared some details on how VarSeq, our flagship clinical analysis software, runs natively in VSW in his blog “Bringing Variant Analysis to your Browser with VSWarehouse 3”. Aidan Bickford, a Senior Fullstack Software Engineer at Golden Helix, also did a deep dive on VSW3’s various tools to bring all of your data and pipelines together in his blog, “VSWarehouse 3 as an Integration Platform”. Today, I’d like to synthesize some of the information above into a clear picture of the user experience for existing users migrating to VSW3 and new users developing pipelines or replicating existing pipelines within the platform.
VSWarehouse 3 in Three Parts
Let’s break VSW3 into three conceptual levels: (1) the deployment infrastructure, (2) the workflow development interface, and (3) the application-running interface where end-users launch VarSeq and other associated tools. The first level is the infrastructure on which VSW3 is deployed, i.e., where data is stored and processed. This can be cloud storage and computational agents, on-premise storage and computational resources, or a mix of both. Primarily, IT personnel and bioinformaticians will be interfacing with this level, and the details of the deployment are completely abstracted from the end-users, i.e., variant analysts and clinicians. We won’t go into more detail on this level of deployment in this blog, but the main takeaway is flexibility. Whether your lab wants to preserve existing infrastructure, migrate to the cloud, or explore the pliability of having both options, VSW3 can integrate all of your underlying infrastructure into optimally running your workflows.
Next, we have the workflow development interface. This is primarily the realm of bioinformaticians. At a high level, within the VSW3 environment, users can define the inputs, outputs, and run environments for each component of a pipeline that yields a VarSeq project where end-users perform clinical analysis. In some of the resources linked above, we describe how these workflows include essential tools like API integration with external processes and the ability to dynamically allocate computational nodes for each component of a pipeline. Furthermore, bioinformaticians can directly interface with the back-end, seamlessly porting their existing workflows to run at the click of a button in VSW3.
Lastly, let’s dive into the end-user experience, the culmination of all of the work described above. Fundamentally, everything is abstracted to the point where the clinician or variant analyst is interfacing with VarSeq and VSClinical exactly as they would have prior to the VSW3 paradigm. Users have all of the same capabilities that they are used to, with improved integration of data sources handled on the VSW3 back-end. Interfacing with a project, reviewing results, and generating a clinical report are exactly the same as before. However, advanced integration tools like shared assessment catalogs and data sources are now the default deployment strategy, saving end-users the difficulties associated with navigating pitfalls like permissions, data security, and network issues.
Looking Forward
In summary, we’ve developed the tools to flexibly upgrade and deploy existing pipelines and infrastructure to VSW3 for existing and new customers. Our roadmap includes continuing to develop ready-to-go workflows for customers looking to add on new capabilities or instantaneously port current strategies. As we continue to release new tools in the realm of cancer analysis, pharmacogenomics, and germline analysis, we will be developing automated workflows for these in VSW3. Hence, users can expect an increasingly integrated and seamless experience with the same level of support they’ve come to expect.
Stay tuned as we release more information on VSW3 and start releasing more workflows. As always, don’t hesitate to reach out to [email protected] if you are interested in a demo or [email protected] with any questions, concerns, or suggestions.