Expanded use of New Microscopy Technology Requires an Innovative Approach to Storage

April 17, 2017

Life sciences organizations have been grappling with large and growing volumes of data for years by conducting research using the latest generation of sequencers, microscopes, and imaging systems.

But what happens when new equipment is expected to require a four-fold increase in storage? That was the situation the Van Andel Research Institute (VARI) recently found itself in. Already a leading life sciences research institute, VARI enhanced its capabilities with a new state-of-the-art cryo-electron microscopy (cryo-EM) facility. The centerpiece of the facility is an FEI Titan Krios from Thermo Fisher Scientific, the world’s highest-resolution, commercially available cryo-EM.

A new phase in life sciences research

VARI, which is part of Van Andel Institute, is at the forefront of what industry experts see as a next step in research that explores the origins and treatment of diseases. While cryo-EM technology has been used for decades, the newest instruments can quickly create high-resolution models of molecules, something that was not attainable with other techniques before. This gives researchers a powerful new tool to more quickly and more precisely see some of the smallest yet most important biological components in their natural state.

Managing and analyzing such microscopy imaging data has moved life sciences computing beyond traditional genomics and bioinformatics and gets into phenotyping and correlation and structural biology. All of this work requires more computational power and much more storage capacity. To that point, cryo-EMs can generate up to 13 TBs of data per day. This represented a storage and data management challenge for the institute. Other organizations that move into this type of research can benefit from the lessons VARI learned.

Keeping the HPC workflows running

VARI has a 20-year history of conducting biomedical research and providing scientific education. Its focus is on improving health and enhancing the lives of current and future generations. Using state-of-the-art technologies and instrumentation, the institute’s scientists, educators, and staff work to translate discoveries into highly innovative and effective diagnostics and treatments. The institute needed a powerful HPC and storage environment to serve teams of scientists with diverse research demands and aggressive project timelines.

The addition of the powerful cryo-EMs built on this tradition. The cryo-EMs enable VARI scientists to see the structure of molecules that are one-ten-thousandth the width of a human hair, and is expected to quadruple VARI’s storage requirements. The institute’s scientists also are conducting data- and storage-intensive trailblazing molecular dynamics simulations and large-scale sequencing projects in the search for new ways to diagnose and treat cancer, Parkinson’s, and many other diseases.

What was needed was an infrastructure that would allow the institute to elevate the standard of protection, increase compliance, and push the boundaries of science on a single, highly scalable storage platform.

After determining that an IBM® Spectrum Scale™ (formerly known as GPFS) parallel file system was the way to meet current and future storage needs, VARI chose DataDirect Network’s (DDN’s) GS7K® parallel file system appliance with enterprise-class features, including snapshots, rollbacks, and replication. The institute also selected DDN’s WOS® storage to provide an active archive for greater global data sharing and research collaboration.

Most important, the solution simplified data tiering between the GS7K and WOS, providing a single storage system that enables instrument and other research data to be ingested, analyzed, and shared in a manner that addresses both performance and cost-efficiency. In addition, DDN’s OpenStack® driver significantly streamlined storage integration with VARI’s hybrid on-premises and cloud computing environment.

Benefits abound

The new storage solution is helping in a number of ways.

The end-to-end solution replaced fragmented data silos with powerful, scalable centralized storage for up to 2PB of instrument and research data. According to Zachary Ramjan, research computing architect for Van Andel Research Institute, consolidating primary data storage for both state-of-the-art scientific instruments and research computing offers better protection for irreplaceable data while reducing infrastructure costs considerably.

“We’ve saved hundreds of thousands of dollars by centralizing the storage of our data-intensive research and a dozen data-hungry scientific instruments on DDN,” said Ramjan.

With the highly scalable storage solution, the institute is prepared to accommodate the expected 13TB a day of data generated using its cryo-EM technology. The solution employs a tiered storage approach. New data goes straight into the high performance DDN GS7K  tier.

As the data “cools” and investigators move to new projects, the institute may still have to retain the data due to obligations or the user wants to keep it around. At this point, the data is automatically moved to a lower performance and more economical tier. This is the WOS controlled tier. It’s where much of the cryo-EM data will end up after initial processing.

Data movement is controlled by policy capabilities in the file system. Automating data flow in this way greatly reduces steps and admin requirements.

The result is that researches get simple, fast access to petabytes of storage for research and instrument data that has the high performance of a well tune parallel file system but the easy expandability of an object storage solution all-in-one. And the solution meets the institute’s exponential storage growth and active archive requirements of that data. The end-to-end DDN solution thus provides the scalable storage capacity VARI needs to keep pace with the increased use of cryo-EM and next-generation sequencing technologies.


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