ENPICOM Supports Faster Insights for Therapeutic Antibody Discovery Using AWS

Dutch bioinformatics software engineering company ENPICOM provides powerful data analysis software and customized solutions to decode the immune system and improve human health. This involves managing large amounts of data from samples that typically generate millions of DNA sequences. The analysis requires significant amounts of computing power, which can be expensive. Looking for a cost-efficient solution that would offer secure data management and speed up the analysis, the company migrated its cloud-based IGX Platform to Amazon Web Services (AWS). Using AWS, ENPICOM has improved scalability and performance by 3 times compared to its previous systems. The company has also increased its ability to innovate, and enhanced user experience for the scientists who use its platform to develop insights that can translate into new medicines, vaccines, and antibody-based therapeutics.

ENPICOM works with partners to develop tools and validate applications that bridge the gap between immune repertoire sequencing (Rep-Seq)—a way to understand the different types of antibodies and proteins that are an essential part of an individual’s immune system—and the insights that lead to better understanding of the adaptive immune system.

These insights are needed to develop new vaccines, discover novel therapeutic molecules that could prevent disease, detect disease or relapses early, and create highly targeted treatment options for patients suffering from cancer, immune disorders, and other debilitating diseases.

However, managing immune Rep-Seq data is complex and the amount of publicly available sequencing data is only growing. “Our platform is incredibly heavy to run from a computational perspective,” says Vadim Galaktionov, head of software development at ENPICOM. “To democratize the Rep-Seq data analysis space, we need to offer a service to our customers in an economically sustainable way.”

Another driver for the migration was the fact that many of ENPICOM’s customers already used AWS, meaning customer onboarding and data sharing would be simpler and more efficient.

Migrating the IGX Platform to AWS was quick and seamless. The entire process took a total of 6 weeks, from the initial call with AWS to the final cutover, and required only a small team at ENPICOM to manage it. During the migration, development work continued as normal, with just a few hours of downtime.

The IGX Platform now runs on Amazon Elastic Compute Cloud (Amazon EC2), which provides secure and resizable compute capacity. It also uses Amazon Elastic Kubernetes Service (Amazon EKS), a managed container service to run and scale Kubernetes applications, and Amazon Elastic Container Registry (Amazon ECR) to store, share, and deploy container software. ENPICOM found the support and high-quality documentation provided by AWS to be invaluable during the migration.

Galaktionov immediately noticed the excellent levels of support from AWS. “From the first moment we reached out to AWS, we were surrounded by an incredibly competent team of people who were not only interested in bringing us on board but were interested in making us succeed,” he says. “They wanted to make the migration successful and help us to grow our business after that.”

The ENPICOM team checks in weekly, and sometimes daily, with AWS account managers and solutions architects, who are always able to refer them to the right people to solve problems or provide new capabilities.

The AWS implementation includes managed services for the data layer, which Galaktionov says boosts database performance. For example, using the Amazon Aurora relational database service, ENPICOM’s PostgreSQL databases can run up to 3 times faster than before, speeding up processing times. “If I can get more performance without taking on more engineering work, that’s a win for any engineering manager,” says Galaktionov.

Another benefit of the migration to AWS is ease of management. Day to day, the AWS infrastructure is managed by just a single member of the ENPICOM IT team. Despite the migration to AWS driving a stronger sales pipeline, there have been far fewer governance questions to deal with, meaning Galaktionov can spend more time on higher-value aspects of his role. “Now I can focus on actually heading our software department and taking the IGX Platform to the next level,” says Galaktionov.

Running on AWS has also promoted innovation. The capabilities of AWS allowed for the development of a new, specialized application for the IGX Platform. The application means that researchers can significantly improve their pool of antibody candidates and de-risk their candidate development process.

The application uses peer-reviewed algorithms to predict highly relevant properties—called sequence liabilities—of antibody candidates. By assessing sequence liabilities, researchers can make informed decisions about which antibodies have the best developmental profile, and are therefore the least likely to pose challenges during production and clinical development. By screening for sequence liabilities early in the discovery process, less time and fewer resources are wasted on pursuing unfit candidates. This greatly increases the chance of successfully bringing a new therapeutic product to market.

Using AWS, ENPICOM can now scale up or down as needed. The backend of the IGX Platform takes care of the computational heavy lifting. This means that the company can provide an intuitive, highly scalable workflow that can assess sequence liabilities for thousands of sequences with just a few clicks.

ENPICOM is also working on its next-generation data layer, which will use the Amazon Athena data querying service to handle almost 100 times more DNA data. It will also incorporate machine learning services such as Amazon EMR to run big data workloads and Amazon SageMaker to build, train, and deploy machine learning models—which will help bring products to market. “I trust that, no matter how much we grow, AWS will grow with us,” says Galaktionov.