Solving the Challenges of Biological Sample Management

Biological sample management is the process of registering, organizing, storing, and tracking biological specimens—and the data connected to them—through their full lifecycle. That means knowing what each sample is, where it’s stored, how it’s been handled, and who has accessed or changed it over time.

As biobanks and research programs grow, sample volumes increase and workflows get more complex. This matters for biobanks, translational research, and clinical studies—especially when samples span multiple sites, timepoints, and storage conditions.

A strong biological sample management approach helps teams protect sample integrity, reduce errors, and maintain traceability and compliance—without slowing down the science.

With the right software, biobanks can address these challenges while ensuring quality, compliance, and accessibility. Below we explain some of the key challenges of biological sample management and how the right software can help.

 

Contents: Sample Management Challenges | Solutions for Managing Samples | LabKey’s Solution

 

Challenges of Biological Sample Management:

Biological samples are valuable—and often limited. As collections grow and samples move across people and storage locations, these challenges become harder to manage. Done well, teams can answer in seconds: What do we have, where is it, what’s its history, and can we use it?

Everyday operational challenges

• Sample integrity: Handling and storage variation can degrade specimens and affect downstream results.
  • Example: temperature excursions or repeated freeze–thaw cycles can compromise results.
• Inventory control: Manual tracking drifts from reality, leading to misplaced samples and duplicate IDs.
• Traceability: Without a complete history, it’s hard to confirm provenance across aliquots and derivatives.
  • Example: connect a parent sample → aliquots → assay results to support reproducibility.
• Findability: Teams waste time when they can’t quickly locate the right sample or confirm availability.

Challenges that increase with scale

• Compliance and auditability: Reviews get slow and risky when access, edits, and custody aren’t consistently recorded.
• Accessibility and collaboration: Work slows when sample data is siloed or permissions are unclear across teams.
• Scalability: Processes that work for one freezer or one team often break at higher volume or across sites.

 

How Can Software Help Manage Biological Samples?

Sample management software helps biobanks overcome the challenges of managing a large and diverse collection of biological samples and is essential for modern biobanking.

Core capabilities of helpful software include:

• Register samples in a central registry: Keep IDs, metadata, and status consistent across teams.
• Track storage locations: Map freezers → racks → boxes → positions so samples stay findable.
• Capture lineage: Connect parent samples to aliquots, derivatives, and downstream results.
• Record activity history: Log moves, check-outs, consumption, and disposal with user + timestamp.
  • Example: capture who checked out a vial, when, and why.

Controls that help teams managing biological samples scale:

• Manage permissions: Ensure the right people have the right level of access.
• Maintain audit trails: Keep a reviewable record of changes for quality and compliance.
• Standardize workflows: Use required fields and validation to reduce inconsistency.
• Improve search: Find samples quickly by metadata, location, study, or status.

Although not every sample management software is well suited for biobanks, the right sample software should be able to help in the following areas:

Biological Sample Tracking and Management:

Software can assist in the tracking of samples, reducing human error in registering, receiving and locating samples. At a minimum, biobank and sample management systems should manage inventory in real-time, showing which samples are available, where they are stored, how they have been used and by whom. 

Integrated Data Management:

Sample management software can integrate sample data with associated metadata and experiment results, ensuring that all relevant information is easily accessible and linked to the correct sample. Unifying samples with their associated data also improves the efficiency of research efforts by minimizing the systems where biological sample information is stored. 

Regulatory Compliance and Reporting:

Sample management software can help ensure your lab’s compliance with legal and ethical standards, capturing the who, what, when, where and how of your biospecimen lifecycle. It will maintain proper records and data protection measures and allow easy, but secure, access to these records. Look for options to generate reports for audits and reviews, access and track chain of custody, and flexibly query audit logs. 

Access and Distribution Management:

Role-based access, permissions and system defined workflows in software can help handle requests for biospecimens, track usage, and ensure proper approvals are in place before sample distribution. Additionally, searchable lab inventories allow the correct team members to quickly locate and check the status of samples, whether they are in use or stored in the freezer.

Scalability and Flexibility:

Good software solutions can scale with the growth of a biobank, providing fast-acting data storage and robust searchability beyond the capabilities of spreadsheets. There’s also built-in flexibility to adapt to new types of samples, higher volumes, and changes in processing methods that naturally occur as a lab or biobank grows.

 

How Can LabKey Sample Manager Help?

LabKey Sample Manager helps labs manage biological samples from intake through downstream use. It supports accurate inventory, consistent sample data, and end-to-end traceability—so teams can scale without losing control of where samples are or what happened to them.

What you can do with Sample Manager

• Register and receive samples: Capture IDs and standardized metadata at intake so every sample starts with a complete record.
• Track aliquots and lineage: Document subsamples and parent-child relationships as material is split or processed.
• Manage storage locations: Map samples to freezers → racks → boxes → positions, and keep locations current as samples move.
• Support chain of custody: Record check-outs, transfers, shipments, and other handling events with user + timestamp.
• Integrate sample data: Connect sample records to related data to keep context intact across systems and workflows.

Sample Manager can be configured quickly to fit your lab’s sample workflows and protocols.

Learn more and take a tour of Sample Manager here!