Summary

BioTeam partnered with a prominent clinical diagnostics organization to modernize its digital foundation. This engagement developed a high-level, cloud-smart, modernized strategy for the company’s existing digital backbone, specifically targeting digital image analysis and DNA sequencing to enhance efficiency and oversight and add new diagnostic capabilities. 

Key strategic recommendations from the project included:

• Modernize and incrementally migrate existing bioinformatics pipelines to the cloud, beginning with the highest-volume pipelines.

• Address storage, networking, and accumulated technical debt within the existing on-premises high-performance computing (HPC) infrastructure.

• Restructure the internal organizational model by establishing a specialized Scientific IT team to bridge the gap between bench science and cloud infrastructure support.

• Prototype and evaluate cloud deployment of commercial AI tools and integrate on-premises systems while building a dedicated AI-driven image analysis and QC capability.

 

Our strategic roadmap was designed to extinguish operational bottlenecks, transforming a fragmented infrastructure into a unified digital ecosystem that increases capabilities and accelerates the transition of diagnostics from the lab to the clinic.

Challenge

The biomedical diagnostics market is highly competitive, with companies continually evaluated by clinicians for price, accuracy, time to delivery, and innovation. When BioTeam partnered with a leading organization in the clinical laboratory industry, the team encountered critical challenges: 

• Distributed sample collection and the need for uniform diagnostics regardless of sample origin.
• Required adoption of new methods, including those using neural networks and other AI technologies.
• Requirement to maintain multiple different technologies to analyze images of different types, liquid samples of different types, and tissue samples of different types.
• Requirement for analysis and verification by expert pathologists, usually working from remote locations.

Approach

The assessment involved a one-day on-site workshop, interviews with stakeholders, and the final delivery of findings and strategic recommendations for this cloud-smart transformation, including a roadmap to migrate key bioinformatics and imaging workflows to the cloud while optimizing current on-premises HPC and storage.

BioTeam also examined staff responsibilities and recommended consolidating and strengthening the research computing staff and their infrastructure.

Outcomes

The BioTeam assessment delivered a strategy that would:

• Transition to a cloud-centric approach for sequencing and imaging to shift IT costs from capital expenditure (CapEx) to operational expenditure (OpEx), and to gain efficiency, scalability, and supportability.
• Incrementally migrate existing bioinformatics pipelines to the cloud. Standardize on NextFlow, starting with a key, high-volume pipeline, to modernize and improve its robustness, efficiency, and scalability.
• Prototype and evaluate a pathology image annotation system in AWS with AI-driven image analysis and QC capabilities. 
• Build a dedicated Scientific IT team to provide holistic support and innovation across multiple locations.
• Maintain and improve on-premises infrastructure until the cloud transition is fully complete.
• Increase network and storage performance in key data centers.
• Drastically reduced deployment time.
• Built-in change tracking and automated validation records to simplify and accelerate regulatory submissions.
• Our infrastructure-as-code approach and Continuous Integration / Continuous Deployment (CI/CD) automations replaced error-prone manual deployments with repeatable, auditable pipelines.