How a Clinical Research Firm Achieved AWS Compute at Scale

  • September 20, 2019
NTT DATA Blog 15

As a privately held clinical research organization, our customer provides research services across the entire drug development process to its clients. Its trusted research is used by leading companies within the pharmaceutical, biotechnology, and medical device industries as well as by government and academic organizations. We were approached to help it with two specific — yet different — goals it was hoping to achieve through a new AWS infrastructure.

First, the company wanted to update the system its internal team of research scientists used for data analysis as the team’s large data-related demands had outgrown its on-premise system. Second, the company had bid on a federal government project that should they win it, would require cloud capabilities, such as a secure, elastic, high-performance computing environment. While the federal government project could be announced at any time, the teams had a looming deadline to meet.

Moreover, to meet its pharmaceutical and government clients’ compliance needs, this research firm needed its new environment to be FISMA and NIST 800-53 compliant and have security best practices built in. For both its internal and external audiences, the firm required that the new environment offer scalability and high availability that will meet both audience’s big data needs. Last, the environment needed to support two technologies the company uses regularly: Galaxy, a solution for building distributed apps for fine-tune control over data placement, and RStudio’s data analysis software.

AWS Compute at Scale
The NTT DATA team worked closely with this clinical research company to fast-track the new, compliant AWS environment running Galaxy and RStudio. The teams started by creating an AWS foundation for the company’s high-performance computing environment to be used by its research scientists. An almost identical environment was created for the federal agency to explore, using data from real studies.

To start, they created a service-agnostic landing zone where the firm’s services will deploy. To build the landing zone, the teams created an AWS CloudFormation template that defines VPC, Subnets, NAT Gateways, Internet Gateways, Security Groups, and NACLs. In this way, the firm can track changes and reproduce the same landing zone in different environments — production, development, and staging — growing consistency and reliability.

AWS CloudFormation templates were also used to define the infrastructure for RStudio and Galaxy, ensuring the right number of instances, S3 bucket configurations, and more. All AWS CloudFormation templates are available in the company’s new AWS CodeCommit service repository.

Based on work by Matt Chambers at Vanderbilt University, the team built a single Galaxy cluster within AWS (that can be easily reproduced across its environments) using CfnCluster, Amazon’s framework that deploys and maintains high-performance computing clusters on AWS. Using CfnCluster, the team was able to create a single Galaxy cluster for the company that would scale based on the number of jobs in the queue.

This is important to the scientific team as:

  • All scientists could now use the same cluster and not be concerned about tracking and managing an unwieldy number of clusters.
  • Scaling for jobs, rather than CPU usage or other compute metrics, ensures scalability that directly addresses their needs.
  • CfnCluster supports spot instances, allowing the team to take advantage of steep discounts on resources.

In all, these steps have helped the research firm easily share its work and results using Galaxy, in a scalable environment that significantly decreases costs while increasing the research team’s productivity.

Security and compliance
For security, AWS CIS Framework recommendations and NIST 800-level controls were implemented as a moderate baseline. These controls ensured security best practices were built in through:

  • Data encryption in transit and at rest.
  • Disaster preparedness with EC2 instance back-ups — using a Lambda function — which are then deleted after a defined retention period.
  • Amazon CloudWatch monitoring for defined metrics and the collection of aggregate application logs for review and debugging, as needed.
  • Site-to-site IPSec tunnels to securely enable communication between the Internal Production, Internal Service, and Internal Staging accounts, and the on-premise network.
  • IAM and CloudTrail-ensured separation of duties.
  • An AWS Inspector review of all EC2 instances for vulnerable software.

Through these mechanisms and more, the teams built controls into the architecture to ensure the new environment is secure and meets NIST 800-53 and FISMA standards.

Ensuring success
In addition to a secure, scalable AWS environment, knowledge transfer was a key gating factor of success, with this company wanting to efficiently manage its own infrastructure moving forward. As a result, we taught the customer’s teams along the way ‘how to fish’ to ensure they could effectively manage and extend the infrastructure moving forward. The teams then worked together to train the research scientists on their new Galaxy environment.

AWS HPC benefits
This company’s scientists — and its potential federal government customer — can now effectively analyze critical data in a new high-performance computing environment. And, the secure AWS environment meets the company’s FISMA and NIST compliance objectives.

Moreover, fully committed to AWS, the firm now has an optimized architecture to maximize AWS benefits for decreased maintenance. In the past, this firm had to configure its environment manually and if it was out of capacity, bring it all down and rebuild it. Following the new AWS Galaxy cluster implementation, the company now has a fully scalable cluster where resources can spin up and down based on jobs in the queue, maximizing scientist productivity, reducing costs, and ensuring long-term success.

*This was originally written by Flux7 Inc., which has become Flux7, an NTT DATA Services Company as of December 30, 2019

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Derek Magill

Derek Magill, solution architect at NTT DATA , brings more than 20 years’ experience in IT Engineering with specialization in high-performance computing. Derek currently serves as the Chairman of CELUG, and is the Executive Director of the Association of High-Performance Computing Professionals.

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