Faster genomic analytics from an optimized HPC architecture

Personal Peptides Speeds Genomic Analytics with Optimized AWS Infrastructure

HPC Cloud Computing

Personal Peptides sequences the genome of individuals aiming to manage cancers using immunotherapies. The company’s ImmunoDiet™ program is a nutrigenomic testthat provides oncologists and nutritionists with the information required to create a customized nutrition plan to improve the outcomes of cancer patients.

Cancer can mutate to mimic certain proteins found in food, and consuming these foods has the potentialto suppress the cancer immune system. Similarly, a strategy to avoid foods that may damage the cancer-specific immune system can help boost an ongoing immune system response against cancer. The challenge is thatresearch shows DNA in each individual’s canceris very different. Treatments must be customized for each person. Personal Peptides enables health and nutrition providers to counsel patients to manage their diets according to the individual DNA oftheir cancer with the aim of improving their outcomes

Challenge

  • Secure, compliant HPC architecture to bring solution to market Personal Peptides needed commercial, high performance solutions to process big data at massive scale.
  • Meeting HIPAA requirements and enabling Personal Peptides to control and protect client information along the supply chain was essential.
  • Maintaining competitive advantage through efficient use of computing resources was imperative in the competitive field of biometrics.
  • Managing hardware would not be a viable option; the company needs to remain agile, manage periodic spikes in demand and rely on a self-managing infrastructure.

High Performance Computing Infrastructure

To accomplish this,the DNA must be sequenced, analyzed and compared against other large data sets,requiring massive amounts of computing resources in orderto return information within a reasonable timeframe. While the data analytics could be performed in academic centers where high performance super computers were available for research, the only viable commercial solution was public cloud resources from Amazon Web Services,relying on their HIPAA compliant services to maintain patient privacy.

Even with AWS’s inherent high scalability, computations were estimated to take too long. While the time estimate had been reduced to decades,that was simply still too long.

Rapid Provisioning &
Continuous Deployment

A tenet of DevOps based cloud computing, rapid provisioning is a key component of successful microservices. This company was able to achieve rapid provisioning through greater automation that orchestrated deployments in a secure, duplicable manner. Once components of the firm’s environment were determined, they could be deployed time and again with predictable, repeatable results.

Continuous deployment was achieved through the use of automation, cloud- based services, Docker containers and best practices. Flux7 used these resources to build code delivery pipelines that are secure and agile. In the process, this firm’s developers were able to accelerate the software delivery process, cutting the overall cost of software development, and delivering high-quality code faster.

Specifically, the customer had a unique need in that they needed multiple versions of the same microservice running concurrently. When a customer logged in, the login system would assign them the versions of the microservices that they shall be communicating with. This allowed them to selectively roll new versions of each microservice to different customers one by one, rather than upgrading them all at the same time. The decision regarding which microservice version a customer should use was based on the upgrade cycle they were following. For usability reasons, the customer did not want this information to be exposed to the end user through the URL.

Cracking the Genomics Big Data Challenge

Jahan S. Khalili Ph.D., founder of Personal Peptides and a recognized leaderin the field of nutrigenomics had developed the methodology needed to deliver the ImmunoDiet™, but was struggling to find the expertise that would be required to properly architect an AWS environment that could manage his HPC requirements, let alone fit his need for an efficient, self-managing system.

After finding that a company specializing in providing infrastructure to the biometric industry was unable to provide a solution, Dr. Khalili engaged AWS partner Flux7. Flux7’s full stack experience and deep application and infrastructure knowledge meant a solution that met all of Personal Peptides’ requirements could be readily built. The application architecture included compute clusters for machine learning models, scalable task queues, search indexers and auto-scaling workers. The requirements ofthese applications, as well as the business requirements, needed to be carefully mapped and an AWS architecture was configured to meetthose needs.

Dr. Khalili noted that“Flux7 had a unique way of looking atthe challenge thatI did not find from other vendors. They were able to rearchitectthe entire system and use their partnership with Amazon Web Services to strategically work through any technical or business issues that arose.”

Preserving the Document Chain

Personal Peptides’ client DNA samples are provided to Illumina, a well-regarded DNA sequencer. Illumina’s BaseSpace tool allows researchers to upload massive data sets directly to the cloud for analysis and to store the results long-term with Amazon Glacier. Because of this, the patient’s data never has to leave the secure, compliant environment of AWS, providing an additional level of data protection along the document chain.

Self-managed, Near Limitless Infrastructure

Personal Peptides is now able to create a viable product and bring itto market in a way that meets the needs oftheir customers. By using a massively parallel compute cluster, NoSQL and indexing within Amazon Web Services, Personal Peptides is able to conduct genomic analysis and produce recommendations within a viable timeframe and cost.

The final solution uses a combination of enterprise grade messaging from RabbitMQ,the Celery pre-commerce platform, MongoDB and a proprietary mix of Amazon’s web services to ensure security, privacy and scalability.

“Without the strategic use of AWS capabilities, we would not have had the resources to produce a commercially viable product,” Dr. Khalili said. “Flux7’s deep knowledge of architecture and of AWS has helped us achieve an infrastructure that we’ll be able to maintain ourselves and which will grow with our business.”

Profile

Founded in Houston, Texas, Personal Peptides is the first company to develop a nutrigenomic tool for cancer patients, designed to improve their cancer specific immune system. By bridging the gap between the human immune system and personal genomics, Personal Peptides aims to provide individuals with the tools to sculpt their own immune repertoires.