Contents: Background | Introduction | Challenges | Journey | Why LabKey | Results | Conclusion
Background
The Viral Immunity and Pathogenesis Center (VIPC) at Johns Hopkins School of Medicine is a collaborative group of 10 PI laboratories sharing lab space and working toward common research goals. The center studies the human immune response to viral infections including hepatitis C, hepatitis B, HIV, SARS-CoV-2, and RSV. During the COVID-19 pandemic, the VIPC served as the COVID biorepository for all of Johns Hopkins, processing and storing samples from 10 different COVID studies between 2020 and 2022.
A central focus of the center’s work is the BBAASH cohort (Baltimore Before and After Acute Study of Hepatitis), a long-running prospective study of HCV infection in people who inject drugs in the Baltimore area. Participants are enrolled monthly for blood draws, which are processed into plasma, serum, and PBMCs and stored for long-term use. Their goal is to understand how a subset of individuals spontaneously clear HCV infection, with the ultimate aim of developing a vaccine against HCV.
Introduction
The VIPC managed a biorepository of nearly 300,000 individual samples across 26 freezers and 15 distinct studies on freezer management software that hadn’t been meaningfully updated since 2018. As the lab and its research portfolio expanded, the limitations became harder to work around. When an institutional Windows 11 upgrade threatened to render that software unusable entirely, the lab faced a hard deadline to find a modern solution. They landed on LabKey Sample Manager.
Challenges
Aging software with an upgrade deadline: The lab’s freezer management software offered little functionality beyond a well-organized spreadsheet, and an upcoming Windows 11 upgrade deadline meant the software would become incompatible with their computers.
Decentralized oversight and historical errors: Over more than two decades, dozens of people had interacted with the biorepository in varying capacities and with inconsistent practices, resulting in difficult to correct data quality issues.
Prohibitive upgrade costs: Upgrading to a modern version of their existing software came with costs that were out of reach. The only lower-cost option would have meant a step backward in functionality.
Zero-tolerance for downtime: With samples being actively processed and collected every day across multiple studies, any transition solution had to accommodate continuous operations with no interruption to daily workflows.
The Journey
The VIPC began exploring alternatives to their legacy software in late 2023, eventually landing on LabKey Sample Manager. Given the scale of the biorepository, the data migration was approached carefully and methodically. Rather than migrating freezer by freezer, the team worked study by study, allowing them to focus on the specific data requirements, visit codes, and field structures relevant to each cohort at a time.
Critically, the transition required zero downtime. With samples being actively processed daily, the lab needed to continue operations without interruption while the migration was underway. The LabKey team handled the data transfer directly, making this possible.
Setting up Sample Manager for ongoing use meant designing the system architecture to accommodate the lab’s multi-study complexity: source types, sample types, lineage structure, and a custom status field to distinguish physical freezer samples from processing records. The VIPC also built custom Excel import templates for each cohort, allowing technicians to log samples with minimal manual entry.
Why LabKey
Lineage organization built for complex sample derivation: The VIPC collects peripheral blood but stores its derivatives; plasma, serum, and PBMCs. Sample Manager’s lineage tracking made it possible to represent this relationship clearly, improving the searchability and clarity of the biorepository.
“Having the ability to track multiple sample types and derive one from another vastly improved the clarity of our biorepository.” — Zack Mulcare, Research Project Coordinator, VIPC at Johns Hopkins School of Medicine
Cost model that fit the lab: Sample Manager’s per-user pricing was a strong fit for a large collaborative group where not every member needs direct biorepository access, and with maintenance and support included, it compared favorably to the higher pricing the lab had received elsewhere.
Built-in pick lists for a high-demand environment: With up to 10 graduate students and staff members requesting samples simultaneously at peak times, Sample Manager’s pick list functionality replaced ad hoc email chains and manual tracking with a clear, real-time view of what was checked out, by whom, and what needed to be updated.
Powerful search and filtering: The Sample Finder and bulk ID search tools gave the team fast, flexible ways to locate samples across a massive repository. The lab could search by study, infection status, visit date, or a specific list of participant IDs.
Detailed audit logging: The audit trail in Sample Manager is more detailed and accessible than what the lab had previously, making it easier to identify and correct both daily errors and long-standing historical data issues.
End-to-end migration support: The LabKey implementation team managed the data transfer directly, handling the complexity of migrating decades of records while the lab continued processing samples without interruption.
Results
Modernized, searchable biorepository: The team’s historical samples were successfully migrated into Sample Manager, with lineage relationships, study-specific metadata, and data quality issues resolved in the process. The audit trail and lineage view have made it easier to catch and correct both routine errors and historical data issues that had accumulated over decades.
Zero downtime through transition: The migration was completed with zero downtime, allowing the lab to continue daily sample processing across multiple active studies throughout.
Improved daily workflows: Custom import templates allow technicians to log complex multi-study sample batches with minimal manual entry. Saved searches surface the day’s samples at a glance. Pick lists replaced ad hoc email chains for sample requests.
A foundation that has held up: Two years in, Sample Manager continues to support the VIPC’s active research portfolio, accommodating shifting study needs, new collaborators, and evolving aliquot requirements.
Conclusion
For the VIPC at Johns Hopkins, LabKey Sample Manager is now the operational foundation for a biorepository that had outgrown everything the lab had previously used to manage it. A hard technical deadline forced the decision; the result was a system that handles the lab’s full complexity and has held up across two years of active research.
“It’s really just been a fantastic experience and a great addition to our lab overall.” — Zack Mulcare, Research Project Coordinator, VIPC at Johns Hopkins School of Medicine
Hear it first hand from JHU’s VIPC presentation at the 2026 User Conference