Picking the Right Sample Management System for Your Lab

Sample Management SystemFor many labs, choosing a new sample management system can feel like a daunting task. Whether it’s your first time using software to manage your samples, or you are looking for a new sample management system to replace an existing application, there are a few considerations to keep in mind.

Sample Management System Features

When evaluating a system to manage your samples, it is important not to think about whether “it’s the right system”, but rather if it is “the right system for our laboratory’s needs right now and in the future”. 

Think about the features the system offers and how it matches up with your lab processes and workflow. Are the structured that you would have to change your existing lab processes? Do you feel that you require a system with more flexibility so that it can be configured to your existing sample management processes? Beyond your current lab operations it is also important to consider the future of your lab – do you plan to introduce new assays, processes, or sample tracking procedures, and will the system be able to handle those? Do you need freezer management features to help manage sample storage?

Aside from features, you should also think about how much effort it will take for your team to implement and configure the new system. 

Sample Management System Pricing

The price of the sample management system is also an important consideration. Make sure you are aware of the factors that determine system pricing. This may include pricing tiers based on the database size, number of users, number of samples, availability of certain features, or other price-determining factors. Make sure you are comfortable with any potential increase in cost as your lab grows and your needs change. This can help prevent an unexpected and significant increase in cost at a certain capacity. Making an effort to estimate usage, including users and amounts of data, prior to choosing a system will help you be a more informed buyer and help plan for the future. 

Adopting a Sample Management System in the Lab

Once you feel comfortable with the feature set and cost offered by a particular solution, the single-most important factor in implementing the software is gaining adoption within the lab. 

Incorporating a new sample management system into the lab can be arduous and challenging. Scientists are used to working in a way that is most efficient for them, and introducing a new system may be disruptive to their normal way of operating. To minimize this disruption and foster adoption of the new system, make sure to include the end-users in the lab during the evaluation process. Allow them to test their scenarios and evaluate usability. Create an environment where their feedback is valued and taken into consideration, and ideally choose a system that helps boost their efficiency and complement existing processes. Choosing software that provides tools for data validation, integration and reporting are all good ways to help scientific efficiency move in the right direction. 

Once you have chosen a sample management system, determine an implementation plan that will work for the group, and allow for some trial and error. Pick one or two lab processes that can be moved to the new system, gather feedback and make improvements as needed before implementing a new set of processes. Have a concrete timeline that will empower users to fully test the system and provide time for feedback and checkpoints. 

Product Highlight: LabKey Sample Manager

LabKey Sample Manager is a feature-rich and intuitive sample management software designed to boost the efficiency and productivity of your lab. Easily track samples, manage their lineage, define laboratory workflows, and unify your samples with assay data. Learn more about Sample Manager using the links below:

Sample Tracking – End-to-end sample tracking features including chain-of-custody tracking,  sample types and sources, and lineage views

Lab Workflow Management – Use workflows to standardize lab processes and manage ongoing work in the lab

Freezer Management – Manage sample storage and freezer capacity using an intuitive interface

Sample Data Integration – Integrate assay data with your samples and assign metadata for a complete picture of your ongoing experiments 

Explore Sample Manager – Sign-up for a tour ofLabKey Sample Manager!

3 Tips for Tracking Lab Samples

Complete and efficient lab sample tracking is a must for any well organized laboratory. With a multitude of samples being received, aliquoted, having assays performed and making their way through the lab, it’s easy to see why a lab needs tools and procedures for managing sample tracking. A few general tips for tracking samples include:

  1. Standardize sample naming conventions that are both unique and meaningful. And of course, make sure they fit on the label!
  2. Capture sample metadata that makes sense for your lab, workflow, and for the sample. Make this part of your sample registration procedures and review the data points to be captured with your team to make sure your team is aware and engaged in the process.
  3. Consider when and how the registration of new samples should be done in your lab setting. Are samples registered in bulk via an upload of an Excel spreadsheet or are samples entered individually and registered directly into the sample management software? Alternatively, can you anticipate what samples you’ll be receiving, and can register them ahead of time and mark them as received once they come into the lab? Standardizing the initial sample registration procedures ensures that your sample tracking gets off to the good start.

Tracking lab samples and chain of custody with LabKey Sample Manager

By implementing the lab sample tracking tips above, you can also start thinking about how to track the chain of custody of a sample using LabKey Sample Manager. One way to do this is by viewing the audit log at a macro level to see what’s happened in the system. Each entry tracks the user with a date/time stamp for full-featured auditing. Although this meets many compliance requirements, it is often burdensome to look through the many entries in the system to track down the actions around a single sample.

A much better way of tracking sample chain of custody is using the Sample Timeline feature within the application. Using this feature, users can see and analyze specific events for a sample- starting with when (time and date) a sample was registered and by whom (user).  Also tracked and viewable on the timeline are any metadata changes, assays performed, and the addition of a sample to a particular workflow job. 

Viewing the timeline for an individual sample provides a comprehensive look into the chain of custody of the sample within LKSM in one easy place. This feature can be used as an auditing mechanism, or just another way to track and understand the context of your sample in the lab.

Click here to explore the Sample Timeline in LabKey Sample Manager

LabKey Biologics for Cell Line Development at Janssen Pharmaceuticals

[vc_video link=”https://www.youtube.com/watch?v=AcUj-EN254U” align=”center”]Developing biopharmaceuticals is an increasingly important endeavor in the drug discovery efforts of almost every major pharmaceutical company. High-yield, stably expressing cell lines are of critical importance for economically viable biopharmaceutical production processes. Tracking CLD processes can be challenging due to the number of clones generated, as well as the high number of tests performed to identify producer cell lines suitable for industrial, large-scale manufacturing processes.

In this presentation at the LabKey User Conference, Bo Zhai of Janssen Research & Development explains how he implemented LabKey Biologics to map the entire cell line development process with proper lineage tracking. The platform also assisted in associating the molecule entity as well as analytical testing information with samples at different CLD stages to effectively reduce the clone selection timeline.

About LabKey Biologics

LabKey Biologics is a flexible LIMS software platform providing biopharmaceutical researchers with an intuitive suite of tools for biological entity registration, workflow management, and integrated data exploration. The platform provides researchers with a complete data landscape by tracking generations of proteins, plasmids and physical samples, and connecting design data to related assay results. Learn more about LabKey Biologics by exploring the features below:

Bioregistry – Capture structured data of all biological entities and samples.

Electronic Lab Notebook – Create data-rich notebooks with a fully integrated ELN.

Biologics Assay Management – Integrate experiment data from any assay, connecting results to sample details and lineage information.

Biologics Workflow Manager – Manage and optimize your Biologics development processes

Media Registration – Define standard recipes and available raw ingredients to facilitate consistent media preparation.

Request a Demo or Start a Trial to learn more about LabKey Biologics.

Tutorials: LabKey Server SDMS for Research Studies

The LabKey Server platform can be easily configured to manage longitudinal study data allowing for efficient curation, analysis and publishing. These features include data integration, a customizable study framework, quality control workflows, an intuitive visualization builder, manuscript development tools, and de-identified data publishing. 

To help users configure LabKey server to their study data needs as well as to help those evaluating LabKey, we have put together a series of tutorials. You can also try LabKey server using these resources:

>Explore an Example Research Study 

>Start a Trial of LabKey Server

>Design Your Own Study

Research Studies with LabKey Server 

Interactive Data Grids
The LabKey platform provides a graphical user interface to import, query and analyze your research data. Learn how easy it is to chart, correlate, and drill down into your data in this quick online tour.

Time Chart Visualizations
Visually presenting research data in a way that your users can easily answer their own questions can bring your results to life. In a LabKey time chart, the user can change how the underlying data is shown while the live underlying data updates continuously behind the scenes.  In this visualization you can experiment by checking the grouping boxes of the time chart. If you click ‘Edit’ and then ‘Chart Type’ you can access the Plot and Chart Builder to see other data in other ways.

Plot and Chart Builder
In the common plot editor, you can change the type and layout of a chart. On this example, click ‘Chart Type’ to select another plot type, change what data is shown using drag and drop, and use color and shape to add more information. To learn more about building meaningful visualizations within a study see this tutorial- Tutorial: Longitudinal Studies

Quality Control
Tracking the quality of data involves various control measures. LabKey studies can integrate QC status and easily filter to identify approved data as well as data that is in need of further attention. You can see a filtered set of data that has not yet been reviewed by clicking here.

Secure Access
Sharing reports and data with collaborators improves research, innovation, and ultimately patient care.  Protecting the same information from outside access is vital in maintaining patient privacy. Using a trial server, you can use this tutorial to create a working model to see how role and group based access works.

LabKey Supports Total Cancer Care Protocol at City of Hope

City of Hope LogoPrecision medicine for the treatment of cancer involves integrating, aligning and providing access to a multitude of data types. This includes patient data, whole genome or exome sequences, specific tumor sequences, specimen records from dozens of blood draws, biopsies, and more. A recently published case study outlines how LabKey Server provides data integration, analysis and collaboration tools to City of Hope as they treat patients using the Total Cancer Care Protocol. Working within the Oncology Research Information Exchange Network (ORIEN) consortium, the goal of this project is to bring together clinical and genomic data, making it available across the entire City of Hope enterprise where it can be used to improve precision-based therapies.

LabKey at City of Hope

LabKey Server integrates with existing data warehouse systems at City of Hope, provides users with graphical access to querying and reporting, as well as API access for developers and users performing more advanced analysis techniques. There are two main components to how City of Hope is using LabKey Server:

  1. Data aggregation from disparate sources and alignment with patient information
  2. Management of the workflow process itself, including automated import and scripted transformation of data.

More than just a software vendor, LabKey also supports City of Hope’s needs for team collaboration solutions, API development, and workflow integration, with an audit system that supports regulatory compliance. Looking ahead, LabKey solutions offer the expansion and flexibility required for scaling the City of Hope and ORIEN networks into broader use.

Additional Information

Case Study: LabKey Server at City of Hope

LabKey User Conference Presentation: Watch Video

Request a demo of LabKey Server

What’s New in LabKey Server 20.3

LabKey is excited to announce the release of LabKey Server 20.3!

In addition to the extensive improvements described below, LabKey Server 20.3.0 includes an important security update. We strongly recommend that you upgrade your installations. If you are unable to upgrade to 20.3.0 immediately, we have released a hotfix in 19.3.7 found here:  Download 19.3.7

View Full 20.3 Release Notes

Download 20.3 Community Edition

Release Highlights

LabKey Sample Manager is now available with every Premium Edition, offering easy tracking of laboratory workflows, sample lineage, and experimental data.

Plate Assays – Plate data is supported in General assays.

Assay Data Provenance – Track assay data sources.

Trace Query Dependencies – See the dependent and dependee queries within the schema browser.

Sample File Scoped Chromatograms – Display and provide API access to chromatogram-style data contained within Skyline documents.

Sample Comparison Reports ​(Biologics) – Create assay summary reports for selected samples.

Documentation Highlights

FDA MyStudies Documentation Portal – A new portal centralizes documentation for the FDA MyStudies platform.

Installation Documentation – The installation documentation has been improved, including separate checklists for Linux and Windows installations, Linux command examples, clarified requirements for Tomcat configuration, and more.

For a complete list of features please read the 20.3 Release Notes.

LabKey launches Sample Manager – sample management software with data integration and workflow features.

LabKey Sample ManagerLabKey has released Sample Manager, intuitive and powerful sample management software that brings greater ease, efficiency and insight to sample processing within laboratories. The application’s easy-to-use interface provides access to a host of powerful features that address common challenges experienced by labs in the processing and management of samples. These features include user-friendly mechanisms to create samples and efficiently discern sample lineage, workflow features to easily assign and track sample processing tasks,
and features to unify samples with their related experiment data. 

Sample Manager was built with valuable insight from a Product Advisory Council (PAC) made up of academic and biotech laboratories conducting research in various fields. PAC participants focused on providing LabKey with input that informed the development of features to boost sample processing efficiency, provide greater operational control and promote data integrity. 

Read the full press release about the Sample Manager launch by clicking here.

Try LabKey Sample Manager

You can easily begin exploring Sample Manager by visiting the product page and clicking the “Get Access” button in the green section. Once you fill out the form, you will receive an access link in your email to a read-only evaluation version of Sample Manager. Additionally, we will be hosting an “Introduction to Sample Manager” webinar on February 20th at 10:30am PST. Product manager Hannah Brakke will give an overview of the application and conduct a live demo of key features. 

To register for the webinar, please click here.

Google Cloud Integrates with FDA MyStudies

Google Cloud recently announced that they are working to expand FDA MyStudies, an open-source technology platform that supports research organizations as they collect and report real-world data for regulatory submissions. LabKey provides the backend data management for FDA my studies via a dispersed data model that securely partitions personally identifying information to help ensure patient privacy.

Google Cloud FDA MyStudiesWith Google Cloud, organizations will now have another alternative to securely host their deployment of MyStudies. This secure hosting provides organizations with safeguards in the ownership and management of data in their studies including the ability to select which of its researchers and clinicians are able to access what data, and to help optimize the use of that data as directed by participants.

In developing the FDA MyStudies platform, LabKey Server was selected as the data management partner due to its flexible open architecture and ability to securely handle personal health information in a compliant manner. LabKey Server also provides role-based governance of the data stored on the Registration and Response servers to ensure that data is only accessible to authorized users. 

At LabKey, we are excited to learn about the integration with Google Cloud and look forward to having an additional option for secure hosting of the FDA MyStudies platform.  

Additional Resource:
Case Study – FDA MyStudies Mobile App

Centralizing Biologics Assay Data with LabKey Biologics

[vc_video link=”https://youtu.be/2WpQ_ncpsMQ” el_width=”80″ align=”center”]Centralizing biologics assay data so it can be easily viewed and analyzed in a single place is one of the core challenges biotherapeutic research teams encounter. Without centralized assay data, teams must turn to time-consuming and error-prone manual integration methods to collaborate and maximize the value of their analytical data.

LabKey Server’s robust mechanisms for defining assays and uploading assay data are helpful for bringing analytical data into a single system, but our biologics software– LabKey Biologics, takes this one step further and provides valuable structure and connections that help biologics research teams understand how that analytical data fits into the larger context.

LabKey Assay Designs: Standardizing Analytical Data Structures

LabKey Biologics allows teams to define or customize biologics assay designs (many editable assay design templates come pre-defined within the system) to capture assay data in a specific structure. Some teams using LabKey Biologics may need to define only a few assay designs to support their research, while others working in a more complex environment may need to define 100+.

When building an assay design, laboratory teams can choose to add fields specific to batches, runs and results to provide additional context for their data. LabKey supports a wide variety of field types (including integer, float, boolean, and text) and users can configure aliases, validation rules, and a variety of other characteristics for each.

Centralizing Assay Data In the System

Once an assay design has been built in LabKey Biologics, data can be added to the system using that design to provide its structure. There are a number of different ways to load your assay data into LabKey Biologics including:

  • Automatically uploading via the LabKey API
  • Manually uploading spreadsheets
  • Pasting spreadsheet-type data
  • Entering data into a form

The first strategy, automatically uploading, leverages the APIs of LabKey Biologics to allow other instruments or file systems to talk directly to the system. The other three strategies involved a manual process suitable for varying use cases. If you have a large spreadsheet to integrate, you might want to use the manual upload method or paste the tabular data directly into the application. If you just have a couple of values you want to enter, simply entering the data into a form in the LabKey Biologics UI might be the simplest strategy.

Leveraging Sample Lineage for Context

As you know, analytical data generated during experiments is tied to a specific sample. Because the lineage of samples is tracked in LabKey Biologics, the application will automatically query sample lineage when data is uploaded and present relevant biological entities side-by-side with analytical data in the bioregistry. Showing the sequence or molecule information adjacent to the analytical data, allows scientists to easily ask questions of their data and conduct comparisons with other sequences that are seen in different experiments.

Ready to see this functionality in action? Watch the quick look video above. For more information or to request a demo- Click Here

4 Tips for Improving Lab Sample Management Workflows

Research and clinical laboratories alike are continuously striving to improve their lab sample management workflows. As more organizations invest in translational and collaborative research, the need to collect samples with higher integrity and reproducibility increases. By using sample management software to improve their laboratory workflows, labs can generate more reproducible and reliable endpoints while also boosting processing efficiency. Standardizing processes and workflows can help improve identification methods and reduce processing errors within laboratories. 

Common ways to improve your lab sample management workflows include:

  1. Standardize the processes within your lab.
    Developing Standard Operating Procedures (SOPs) for your laboratory sample management increases the reliability of endpoint samples and therefore the assay results. Well-developed SOPs will account for common troubleshooting methods and provide mechanisms for users to document abnormalities. This in turn will provide more insight to groups downstream about the sample fidelity. SOPs also act as excellent training resources for new staff and ensure the entire team is well trained and prepared for managing samples in the lab.

  2. Determine your laboratory capacity.
    Establishing capacity for any workflow is important. Determining the capacity of both your laboratory staff as well as equipment capacity is important to establish limits that will guide the most effective and reliable lab sample management workflow. By evaluating the available capacity of staff and equipment, new insights can be learned to improve lab and sample processing efficiency.
     
  3. Automate where possible. By introducing automation methods, even if they are as straightforward as barcode generation and scanning, you can improve the laboratory capacity as well as reduce the potential for errors. Barcodes in particular will enhance sample identification and minimize additional effort from laboratory staff. Other advanced methods of automation, such as robotic processing, may also provide value but are typically more costly and can increase processing time in some cases.
  4. Deploy integrated systems that help laboratory work. Using software systems in the lab that do not hinder sample management processes, but instead enhance them, is important for gaining adoption and boosting laboratory morale. By having integrated systems that are easy-to-use, researchers can perform work faster with less ramp-up time, and can recognize discrepancies easier. Downstream, integrated systems offer organization leadership the mechanisms to track workflow data over time with the ability to easily adjust workflows to improve processing.

LabKey Sample Manager

Developed in coordination with our lab partners, LabKey Sample Manager has been intuitively designed to boost the efficiency and productivity of laboratories. The application allows for the registration and tracking of samples and their derivatives, as well as the assignment of samples to custom sample processing workflow jobs. This provides a flexible yet standard mechanism of capturing tasks in each workflow, and can act as a virtual record of sample processing. Additionally, Sample Manager allows laboratory staff to easily capture data generated from these workflows and associate them with samples. 

Contact Us for more information regarding Sample Manager.

Related Post: Benefits of Unifying Lab Samples with Assay Data