Table of Contents
Executive Summary
Three of the Netherlands’ largest University Medical Centres—Utrecht, Amsterdam, and Groningen—managed over 9 million biospecimens across 700+ studies using outdated tools like Excel, Access databases, Item Tracker, and LabWare.
These disconnected systems created inefficiencies in data entry and retrieval, compliance risks, and data management challenges.
Key Efficiency Gains from OpenSpecimen
- ✅ Eliminate duplicate data entry via integrations LIMS and Rack Scanners.
- ✅ 50–70% reduction data entry time by building Custom Workflows.
- ✅ 40–50% decrease storage managementacross 100s of freezers.
- ✅ Ability to build Custom Reports by lab users without IT skills.
- ✅ 100% data accuracy in migrated legacy records—spanning multiple decades.
What UMC Biobank Leaders Are Saying About OpenSpecimen?
“Making the transition from our previous system to OpenSpecimen has been a game changer for us. OpenSpecimen has significantly improved the way we track and manage the entire blood processing workflow in our laboratory— from Ficoll isolation to the storage of PBMC cells in our nitrogen tanks, as well as the serum and plasma storage at our -80°C Freezers. OpenSpecimen tracks each step, acting as a protocol guide, so we always know exactly where we stand in the process. It also generates labels and calculates necessary data, making everything more efficient and reducing the risk of errors. It has become an essential tool for ensuring accuracy, consistency, and traceability in our workflow. And finally, OpenSpecimen provides the user flexibility in how to use the system.”
Liesbeth Niemans
Biobank Manager, UMC Utrecht
“At Amsterdam UMC Biobank, OpenSpecimen is becoming more and more the central thread of all processes – from sample management to business operations.”
Jörg Hamann
Chairman, Biobank Platform – Amsterdam UMC
The UMC Biobanking Landscape
Biobanks are vital to the future of medical research. As these repositories scale, their IT management systems often don't. What starts as a small, manageable setup can spiral into a fragmented, error-prone ecosystem when millions of specimens are added over decades.
This was the situation faced by UMC Utrecht, UMC Amsterdam, and UMC Groningen—three of the Netherlands' largest academic hospitals. Together, they held over 9 million biospecimens across hundreds of freezers and supported 700+ active studies.
Each biobank juggled a mix of Excel sheets, standalone trackers, and ageing biobanking software. Manual data entry and freezer inventor was time-consuming and error-prone. And regulatory compliance, critical in biobanking, became harder to ensure.
The need for a new solution wasn’t just technical—it was operational, strategic, and urgent. The hospitals required a platform to unify workflows, integrate with instruments, and scale effortlessly with evolving study designs. After a thorough RFP (tender) process and evaluation of all available solutions, they found that platform in OpenSpecimen.
Biobanking Challenges at Dutch UMCs
- ⚠️ Fragmented systems: Multiple software tools were used for registration, tracking, and reporting, which led to duplication of data and inconsistencies.
- ⚠️ Limited integration: Systems such as GLIMS, box scanners, and freezer software weren’t communicating effectively, creating data silos and inefficiencies.
- ⚠️ High manual workload: Staff spent significant time manually entering and re-entering data, often under tight timelines, increasing the risk of errors.
- ⚠️ Inflexibility: Legacy platforms could not adapt to the evolving needs of study designs or keep up with regulatory changes, limiting future scalability.
- ⚠️ Compliance gaps: Without proper audit trails and tracking mechanisms, maintaining accountability and ensuring compliance became increasingly difficult.
Three UMCs, Three Journeys: Customizing OpenSpecimen for Local Success
OpenSpecimen provided a flexible, modular platform designed to integrate with existing tools and scale with study complexity. The Krishagni team worked closely with each UMC to devise tailored implementation strategies based on internal needs and technical environments.
UMC Utrecht: Big Bang OpenSpecimen Rollout
UMCU faced urgent system failures and chose a rapid implementation path. In just four months, the team migrated over 3 million specimens across 400+ studies. Broader validation rules allowed the transition to happen quickly without compromising core data integrity.
UMC Amsterdam’s Phased OpenSpecimen Rollout with FAIR Principles
The merged entity of AUMC and VUMC required harmonization of two distinct data models. The team adopted the FAIR data principles—Findable, Accessible, Interoperable, Reusable—enabling consistent transformation. Reusable ETL scripts allowed for phased migration with minimal rework and high transparency.
UMC Groningen Adopts a Gradual, Accuracy-Driven OpenSpecimen Strategy
UMCG, with four legacy databases dating back to 2004, opted for a careful, phase-by-phase migration. Each phase included workflow training, SOP alignment, and role-based access configuration. This strategy maximized accuracy while building user trust.
Custom Built for Impact: Configuring OpenSpecimen to Fit UMC Workflows
The OpenSpecimen team developed several new features, enhancements, and integrations to enable the UMCs to adopt OpenSpecimen according to their local needs.
Workflow Automation for Scalable and Error-Free Specimen Processing
Instead of entering data one record at a time, OpenSpecimen developed custom workflows to enable real-time data entry. This reduced manual effort by 50–70%. Workflow waiting queues ensured that no sample was left unprocessed, improving oversight and efficiency.
Seamless HL7 Integration with LIMS for Real-Time Data Sync
All three UMCs use GLIMS as their LIMS for managing labs. Primary specimens are collected in GLIMS and shipped to central labs for processing. OpenSpecimen is integrated with GLIMS using HL7 v2 protocols, enabling real-time import of participant and specimen data, eliminating duplication, improving accuracy, and accelerating registration.
Boosting Efficiency: FluidX and Ziath Box Scanning Integration
High-throughput biobanks use box scanners to scan entire racks at once. By integrating FluidX/Ziath scanners with OpenSpecimen, users could scan and register boxes of tubes in seconds. Tubes were rearranged, tracked, and linked to digital records seamlessly— reducing processing time by 20–30%. It also improved freezer inventory tracking when specimens were moved or rearranged.
Optimizing Storage and Retrieval Across 100s of Freezers
UMC Groningen manages over 100 freezers and frequently stores/retrieves thousands of specimens. Barcode-enabled workflows in OpenSpecimen allowed faster check-ins, check-outs, and accurate tracking. Features like Carts, box scanners, and Catalogs helped staff find and manage storage locations—cutting retrieval time by 40–50%. Additional reports and features were added in collaboration with UMC Groningen.
Seamless Data Migration with 100% Accuracy
The OpenSpecimen team used detailed mapping, exception handling, and multiple dry runs to manage legacy data transfer. Despite varied formats and data quality, migration accuracy exceeded 98% across all sites. Each UMC had unique schemas and data standards, so strategies were tailored to reduce disruption and ensure smooth transitions.
Empowering Users: Comprehensive Training for Seamless Adoption
A Train-the-Trainer model supported adoption. Local teams created cheat sheets, workflow guides, and video tutorials. Contextual, web-based training improved confidence and reduced onboarding time. Continuous user feedback helped refine processes, address challenges, and increase ownership of the system's success.
Powering Collaboration Across Borders and Institutions
A key benefit of OpenSpecimen has been its support for collaborative and multi-site research. With a single instance of OpenSpecimen, hundreds of collection sites, labs, and repositories can operate seamlessly—despite granular access controls. This significantly reduces friction in procuring and managing specimens across institutions.
The Specimen Catalog feature allows each center to publish selected data for external researchers, streamlining the Request → Approval → Fulfillment workflow. This has enabled the UMCs to collaborate more effectively in national and EU-level research initiatives, where standardized data structures and interoperability are essential.
By aligning with FAIR (Findable, Accessible, Interoperable, and Reusable) principles and supporting integrations across biobank systems, OpenSpecimen fosters better data sharing both within departments and between institutions. This infrastructure lays the foundation for more scalable, transparent, and collaborative research at a national and international level.
Beyond the Rollout: What’s Next for UMCs and OpenSpecimen
With OpenSpecimen fully implemented, the UMCs are now expanding its usage across other biobanks and research groups within their institutions. OpenSpecimen’s flexible licensing terms make it cost-effective to onboard more users and departments without concerns about budget escalation.
The system’s modular architecture supports ongoing scalability and adaptation—enabling each biobank to evolve its workflows without being constrained by rigid software limitations. What began as a digital upgrade has become a strategic enabler for long-term research innovation.
Looking ahead, the UMCs are exploring cloud-based deployments, deeper analytics integrations, and expanding coverage to include new tissue banks and longitudinal studies. OpenSpecimen is no longer just a replacement for outdated systems—it represents a future-ready, agile infrastructure built to support the next generation of biomedical research.
Ready to Transform Your Biobank?
Join leading institutions like UMC Utrecht, Amsterdam UMC, and UMC Groningen in modernizing your biobanking infrastructure. OpenSpecimen helps you unify workflows, reduce manual work, improve compliance, and scale effortlessly with your research needs.