Accelerating Medical Research and Testing

Overview

Challenge

• Speed up SARS-CoV-2 (COVID-19) testing and research, and analyze large amounts of data with flexibility.

Solution

• Deploy converged infrastructure with high performance and automation to run complex analyses faster.

Outcome

• Scales up analytics performance to process large amounts of DNA sequencing data per week
• Speeds up medical research (including COVID-19) by delivering instant insight and eliminating delays
• Transforms static infrastructure into a dynamic, highly automated cluster solution
• Establishes an agile and modular in-house high-performance computing platform

Challenge

Boosting Public Health with Medical Research

Karolinska Institutet is one of the world’s leading medical universities. Its mission is to contribute to the improvement of human health, and generates more than 6,000 peer-reviewed scientific publications per year. The university has a unique position in academia, as the Nobel Assembly at Karolinska Institutet is responsible for selecting Nobel laureates in Physiology or Medicine.

The Centre for Translational Microbiome Research (CTMR) at Karolinska Institutet’s Department of Microbiology, Tumor and Cell Biology is an innovative public-private partnership with Ferring Pharmaceuticals. Ferring Pharmaceuticals is a research-driven, specialty biopharmaceutical company headquartered in Switzerland and with roots in Sweden.

Researchers at the CTMR are working on accelerating research into all aspects of chronic diseases in the gastrointestinal tract and to better understand the impact of the microbiome in reproductive health. The primary goal is to unlock the potential of the human microbiome — the community of microbial organisms found in the body’s digestive systems — to improve treatments and prevent diseases.

Fredrik Boulund, Head of Bioinformatics at the CTMR, explains: “A lot of our work is analyzing lab samples. When we look at DNA sequencing data, the first step is to determine which microbes are in the sample. We analyze the multidimensional microbiome data to understand the community composition. The second step is to look into what the microbes are doing in the sample — what they consume and what they can produce. We need to establish how the capabilities of the microbiome communities in the samples relate to our research questions.”

This research is very compute- and memory-intensive. The CTMR has access to shared high-performance computers (HPC) via the Swedish National Infrastructure for Computing (SNIC). However, it needed access to more flexible compute capacity throughout the year to process large batches of samples that arrive at hard-to-predict timepoints.

“Using external compute resources was a valuable option, but it also limited our productivity,” says Boulund. “The overall workflow provided a slow feedback loop. After planning the analysis, we had to upload the raw data to the shared HPC systems and submit compute jobs to the central queue. Then we had to wait for hours or even days until the jobs had completed — or failed. As we started to outgrow our allocations on the shared HPC systems, we started looking for new options to gain insights faster and more flexibly.”

In 2020, CTMR was also tasked by the Swedish government to move beyond fundamental research and set up a new National Pandemic Centre (NPC). The NPC was launched together with the Science for Life Laboratory (SciLifeLab), an organization supporting molecular biosciences in Sweden. Strengthening Sweden’s COVID-19 response, the NPC analyzed approximately 45,000 PCR-based COVID-19 tests per week. Over the course of the pandemic in Sweden it grew to become one of the largest lab facilities in Sweden for SARS-CoV-2 (COVID-19) analyses. At times the NPC provided up to a fifth of the country’s total testing capacity.

One of the NPC’s key responsibilities is to make advanced technologies and expertise available to researchers working on COVID-19. “When the pandemic work began, we suddenly had to deal with a lot more data,” adds  Boulund. “Our team needed to quickly expand our capability to analyze data so that we could help to advance SARS-CoV-2 research.”

Solution

Delivering Flexible and Fast IT Where it is Really Needed

Seeing the need for more powerful IT resources, Hitachi Vantara approached the CTMR to support COVID-19 research and testing. The CTMR was running IT services and analytics jobs on two physical servers, in a very static configuration with no virtualization or capacity to scale.

The Hitachi Vantara team designed a converged infrastructure solution for the CTMR. In a joint effort, they deployed a Hitachi Unified Compute Platform CI solution in combination with Hitachi Virtual Storage Platform F370 arrays. Hitachi Vantara selected Cisco switches to ensure optimized network performance.

The solution integrates compute, storage, network and management software, and provides a high level of flexibility by using VMware virtualization to adjust resources dynamically. Meanwhile, Hitachi Unified Compute Platform Advisor software simplifies systems management and automates administration tasks. The team can also themselves deploy and use standard HPC tools such as Slurm for cluster management and job scheduling across the virtualized server infrastructure.

Hitachi Vantara worked with its partners Cisco and VMware to offer a comprehensive loan to the CTMR to speed up the implementation. “Hitachi Vantara, Cisco and VMware made a very generous offer,” remarks Boulund. “Their engagement and commercial flexibility enabled us to take advantage of a new, powerful IT solution even before complete funding had been secured.”

The solution meets the strict rules and requirements of the university’s central IT, and is installed at one of the university’s main data center facilities.

Outcomes

Fighting a Global Pandemic and Generating Instant Insights

Thanks to Hitachi Vantara, the CTMR has established an agile and modular in-house HPC platform. By managing its resources with VMware virtualization and Hitachi UCP Advisor, the CTMR has been able to streamline system administration, and automate deployment and system management tasks. The team can quickly and easily reconfigure its cluster by spinning up and shutting down virtual machines for specific computing tasks as needed.

“The automation capabilities of Hitachi UCP Advisor enable us to launch new instances on demand based on standardized templates,” elaborates Boulund. “This approach helps us to tailor instance sizes to processing tasks, maximizing performance across projects on short notice. That means we can be much smarter about our use of resources and in the long term respond faster to requests from our research scientists.”

The solution helps the CTMR to fully leverage next-generation high-throughput DNA sequencing, which is capable of generating very large amounts of sequencing data on a weekly basis. “The practical benefits for our researchers are substantial,” confirms Boulund. “We can generate new insights with much shorter turnaround times. In the past, it could take days or even weeks until we got the results, which slowed down our research dramatically.”

“Crucially, we have used the Hitachi Vantara converged infrastructure solution to analyze and assemble complete SARS-Cov-2 genome sequences. This research will be published to contribute to the global effort of scientists and medical staff to combat the COVID-19 pandemic more effectively.”

Boulund concludes: “In the past, the somewhat cumbersome process to prepare data for analysis on shared HPC resources did not align well with our research needs. Thanks to the support from Hitachi Vantara, we can now analyze larger batches of data much faster, in-house and at any time. Together with Hitachi Vantara, VMware and Cisco, we have modernized our IT and built up a flexible, robust, and highly automated data center. The increased performance is helping us to advance science and inspires our researchers to gain an even deeper understanding of the human body.”