Establishing Sample Management at UW’s Molecular Information Systems Lab (MISL)

Solving sample and data management challenges with Sample Manager

Contents: Background | Introduction | Challenges | Journey | Why LabKey | Results | Conclusion

 

Background:

The Molecular Information Systems Lab is a unique collaboration between the University of Washington and Microsoft Research, with a focus on integrating biology and synthetic biology with computer science tools. The team faced the challenge of managing a diverse range of physical samples and associated data in an efficient and organized manner.

 

Introduction:

MISL was established as a pioneering initiative that brought together biology and computer science. This unique combination of disciplines created a need for a robust sample management system to streamline their research processes. The lab’s research is heavily reliant on maintaining strong connections between physical samples and their associated data. 

 

Challenges:

MISL experienced several sample management challenges:

Lack of Established Systems: Being a relatively new lab founded in 2017 and located within the computer science department, the lab had not adopted many systems common to other biology labs. 

Data and Sample Discrepancies: The lab had multiple researchers working on diverse projects without a centralized system for recording and managing sample information. Information about samples was dispersed across various sources, leading to difficulties in accessing and aligning data associated with physical samples.

Insufficient Labeling: The lab used handwritten labels on sample tubes, which presented problems with legibility and durability over time. Furthermore, the limited space on the tubes made it challenging to include all the necessary information.

High Researcher Turnover: With a dynamic team that included five Principal Investigators, numerous post-docs, graduate students, and undergraduates cycling through projects, samples often got lost in freezers and storage spaces.

 

The Journey:

The team at MISL took these steps to find a sample management solution:

Deciding To Look for an Outside Solution: The prospect of creating an in-house sample management system was daunting and would be a time-consuming task. This led them to explore existing solutions to meet their sample management needs.

Comparing Products: The team explored several sample management systems but found most of them lacking in one or more critical areas. This includes a lack of electronic lab notebook (ELN) integrations, intuitive user interfaces, insufficient support, and limited customizability. 

Implementation: Once MISL had selected Sample Manager as their system, the team began by importing data from CSV files and importing OneNote lab notebook entries into the ELN. The team also ensured that data and information from Quartzy, Benchling, and other programs were set up to feed into Sample Manager, and encouraged researchers to import their own samples and storage locations into the application for any samples they wanted to keep going forward that might have been derived differently than from the manufacturer.

 

Why LabKey:

In their search for the ideal sample management solution, the Molecular Information Systems Lab discovered Sample Manager. This platform stood out for several key reasons:

Robust Sample-Data Connection: Sample Manager allowed the lab to establish a strong two-way connection between physical samples and their associated data, eliminating the need for manual cross-referencing.

Centralized Data: The software centralized all lab data, making it accessible from anywhere, which was crucial for a team that collaborates and works remotely.

User-Friendly and Customizable: Sample Manager’s user-friendly interface and high degree of customizability allowed the lab to adapt the software to their unique research needs seamlessly.

Excellent Support: The LabKey team provided exceptional support, ensuring a responsive and helpful experience.

Electronic Lab Notebook: Sample Manager’s electronic lab notebook functionality allowed the lab to maintain detailed records of their experiments, ensuring transparency and reproducibility.

 

Results:

MISL adopted Sample Manager for their system and has seen these improvements:

Sample-Centric Tracking: The connection between physical samples and their associated data eliminated the need for manual data cross-referencing, resulting in improved data integrity and accuracy. 

Cloud-Based Storage for Sample Data: Sample Manager centralized all lab data in cloud storage. This enhanced collaboration and increased efficiency, allowing access to sample data globally, and eliminating the inefficiencies with dispersed data storage.

User-Friendly and Customizable Interface: Sample Manager’s user-friendly interface and customizability allowed the lab to adapt the software to their unique research, promoting efficiency and adoption of the system within the lab. 

Electronic Lab Notebook: Sample Manager’s electronic lab notebook improved research documentation and reproducibility. Researchers can record and retrieve experiment details, enhancing transparency and making it easier to replicate experiments for validation.

 

Conclusion:

This case study shows how Sample Manager has improved the research operations of the Molecular Information Systems Lab at the University of Washington. By addressing sample and data management challenges, Sample Manager streamlined the lab’s research processes and ensured a robust connection between physical samples and their associated data. Overall, it has become an indispensable tool for a unique research institution bridging the worlds of biology and computer science.

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