Category: About LabKey

The 2020 LabKey User Conference Goes Virtual!

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The annual LabKey User Conference will be held in a virtual format from October 6th to 9th 2020. All four days of the conference and training sessions will be free to attend! As with past conferences, this year will feature informative user presentations, product updates and announcements, educational Tech Talks led by our development team, and our Learn LabKey training sessions. This is an exciting opportunity for attendees to expand their knowledge of LabKey solutions and learn how LabKey is solving the data management, collaboration and workflow challenges faced by life science organizations.

During the conference, the user community has the opportunity to provide valuable feedback and insights to the LabKey team. LabKey Server, Biologics, and Sample Manager have all been developed with significant input and guidance from the scientific research community. This input continues to be the guide by which we prioritize features, optimize user experience within our applications, and make key decisions to deliver the most value to our users. This year we will invite all attendees to participate in UX sessions later in the month for our soon to be released Biologics ELN and Freezer Management applications. 

Agenda

 

Day 1, October 6

  • LabKey Server Update: Learn about new and upcoming features
  • User Presentations:
    • The National Institute of Allergy and Infectious Diseases will present on their use of LabKey Server for COVID-19 research studies
    • Nestlé Health Sciences will present on their use of LabKey Server for assay data and study management
  • Highlight: Currently in use by the FDA, LabKey MyStudies offers capture of informed consent/patient registration on mobile devices to support clinical trials, tools for mobile study design, and compliant hosting infrastructure

Day 2, October 7

  • LabKey Biologics Update: Learn about the exciting product development taking place with LabKey Biologics 
  • User Presentation: Just Biotherapeutics will share their ongoing collaboration with LabKey to develop an Electronic Laboratory Notebook 
  • Electronic Laboratory Notebook Preview: See a live demonstration of our upcoming Biologics ELN, available in early 2021.

Day 3, October 8

  • Sample Manager: Learn about ongoing development and feature updates for LabKey Sample Manager
  • User Presentation: Oregon Health and Sciences University will share how LabKey is used to support translational research
  • Freezer Management Preview: We will demonstrate our upcoming freezer management functionality within Sample Manager
  • Highlight: Using Sample Manager with LabKey Server

Day 4, October 9- Tech Talks

  • ODBC Integrations: Using ODBC to integrate with tools you already know, including MatLab, Tableau, and more
  • Filewatchers: Review the types, mechanics, and customization options of filewatchers in LabKey
  • React and Javascript Development within LabKey: Discuss the recently released API and developing apps within modules
  • Bringing Your Data Together: Integration and harmonization of data with ETLs, linked schemas, and cross-folder queries
  • Best Practices and Benefits of LabKey Hosting: Getting the most out of LabKey with our hosting options
  • Build and Test: Using Artifactory to optimize your build and test process

Seats are limited for the conference, click here to register!

What’s New in LabKey Server 20.7

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LabKey is excited to announce our 20.7 release! This release includes major updates to Sample Manager, domain editor updates and premium LabKey Server features. See the full release notes, and highlights below.

Sample Manager

  • Sample Sources – Track the sources and provenance of your samples, such as subject or lab of origin.
  • Sample Timeline – Track chain-of-custody and capture all events related to a specific sample in a convenient graphical timeline. Timeline information can be exported to Excel, TSV, and CSV formats for auditing purposes.

WATCH WEBINAR: Tracking Samples with LabKey Sample Manager 

Premium LabKey Server Features

Additional LabKey Server Features

Premium Resources

Read More: Release Notes 20.7 (July 2020)

Sample Tracking Software vs Excel: 2 Reasons Why Software is Better Than Spreadsheets

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Due to their wide availability and ease of use, Excel spreadsheets are considered by some labs to be a viable alternative to sample tracking software.  Smaller labs may find spreadsheets more economical and require less training than a sample tracking system. However, Excel spreadsheets have some major drawbacks for managing and tracking lab  samples. Conversely, a dedicated sample management system has features that are necessary as a lab grows and the complexity of tracking samples increases.  

1. Sample tracking software reduces human error

When using spreadsheets for sample tracking, it is very easy for data to go missing or be inadvertently changed. Cells, columns and the data contained within can be deleted or edited, with virtually no tracking of the changes or by whom the changes were made.  Sample management software provides structure to the data captured for each sample and defines how sample data can be changed and by which users. Software also provides an audit trail to monitor and report any changes.

Sample management software has features specifically dedicated to set up rules and restrictions regarding data creation/import and editing. For example, perhaps the volume of a particular sample type should always be a positive number, or the Sample ID is a required field? These features give teams the ability to structure their sample data in a way that makes sense for them. A good sample management software will have the flexibility to allow users to define their own data structures and processes to match the actual lab work, instead of the other way around. 

2. Spreadsheets lack robust security and permissions 

Spreadsheets, unlike sample tracking software or traditional databases, don’t have a detailed permissions model. For example, you may only want certain members of your team to be able to add new rows and not have the ability to edit the columns/metadata. In Excel, you are limited to granting basic read-only or read-write permissions. Sample tracking software allows for more granular permissions to be assigned based on your role in the sample management process. Maybe your Principal Investigator can only read, while the lab manager dictates what type of metadata is captured, and the rest of the lab members can add and update samples as needed.  

Sample Tracking Software- the clear winner!

A well-designed sample tracking software should not require extensive training or a long implementation process. Good software is designed with the end-user in mind and should be intuitive. Sample tracking software also contains a variety of other features that are focused on real-world laboratory sample management processes. 

LabKey Sample Manager is an intuitive sample management software designed to help labs efficiently track samples, define laboratory workflows, and unify samples with assay data. Sample Tracking with LabKey Sample Manager

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

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

Lab Workflow Management – Assign samples to user-defined workflows and monitor the workflow completion status at each stage for every sample

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

Take a tour of Sample Manager – register to see LabKey Sample Manager in action!

Data Management for Translational Research

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Data Management in translational research is key to gleaning insights that lead to personalized treatment plans for patients. Translational research has advanced rapidly in recent years, but patient treatment efforts have been hindered by poor data management practices, error-prone manual workflows, and a lack of collaborative spaces where scientists and clinicians can easily share data and analyses.

With the multitude of data sources and types involved in translational research, teams need flexible data management software tools to help maximize insights and knowledge transfer from bench to bedside. LabKey Server provides the essential tools to overcome the unique data management and collaboration challenges posed by interlinking data from research and patient treatment.

Managing Translational Research Data

Managing translational research data

Proper lab data management in translational research is vital in improving repeatability and reproducibility in experiments. This ultimately leads to more reliable research studies, improved product development and better patient outcomes in a shorter time frame. Data management software plays a central role in managing the integration, quality control, analysis, and sharing of translational research data. In LabKey Server, these features include:

  • The ability to seamlessly connect raw assay data with metadata and the original experiment
  • Built-in quality control tools for recognizing and handling erroneous values
  • A file watcher that automatically loads new data into a new or existing dataset as it becomes available, reducing human interaction and error
  • Compliance tools for ensuring data is reviewed and an electronic signature recorded

Comprehensive Data Integration

Data integration for translational research

Translational research involves many scientists and clinicians compiling multiple data types and sources. These may include deidentified patient data, whole genome or exome sequences, specific tumor sequences, specimen records from patient blood draws, biopsies, and more. Without a data integration hub, this is a daunting and time-consuming process that can potentially slow down research and the downstream treatment offered to patients.  LabKey Server includes these powerful features for integrating translational research data:

  • A compliant study environment with tools that simplify the integration of clinical and research data
  • Automated methods for aligning data from a variety of sources (flow cytometry, Luminex, antibody data, data from electronic data capture systems, etc.)
  • Flexibility and simplified methods for collecting ad-hoc results
  • Tools for comparing subjects across multiple studies

Collaboration and Sharing of Research Data

Collaboration and sharing of translational research data

Sharing data with collaborators improves accountability, innovation, and ultimately the production of new therapies for patients. Hurdles like institutional firewalls and outdated data-sharing methods, like emails, spreadsheets and insecure websites, often hinder collaboration in the scientific community. LabKey Server helps teams collaborate securely by providing:

  • Web-based access to a central platform for data sharing
  • A compliant environment with multi-level permissions, so data sharing is secure
  • The ability to protect PHI data or randomize IDs when sharing information with collaborators

Case Study: City of Hope

City of Hope is a comprehensive cancer care center treating patients using the Total Cancer Care protocol. LabKey Server brings 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 Server integrated with their existing data warehouse systems, provided users with graphical access to querying and reporting, as well as API access for developers and users performing more advanced analysis techniques. 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. 

Read More: LabKey Improves Data Accessibility for Total Cancer Care Protocol at City of Hope

Related Documentation

LabKey Open Research Portal for COVID-19 Research Studies

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Researchers focusing on COVID-19 are using the LabKey Open Research portal to collaborate and share study data. Teams from the Dave O’Connor and Tom Friedrich labs at the University of Wisconsin have started “The CoVen”– a collaboration and data sharing initiative for researchers across a variety of institutions studying the SARS-CoV-2 virus. The diverse data shared in the portal is derived from both human clinical samples and nonhuman primate models. The CoVen teams are contributing to COVID-19 research by focusing on the following key areas:

  • Collaboration on nonhuman primate research studies of the virus. 

Since SARS-CoV-2 causes respiratory disease in infected rhesus macaques and other nonhuman primates, they are a useful animal model for COVID-19.  This includes developing and sharing a Clinical Scoring System and Lab Value Reference Guide to help maintain data consistency across future nonhuman primate COVID-19 studies. Information on animal model development and links to COVID-19 animal model preprints are also made available for reference and exploration

  • Conducting longitudinal viral genome sequencing from human isolates to understand virus evolution.

Viral RNA sequencing from human isolates gives insight into the transmission chain from person to person, and how it differs from city to city.

  • Optimizing assays for virus and antibody detection in nonhuman primate and human clinical samples. 

The development of assays to rapidly detect infections is essential in curtailing the pandemic. The O’Connor Lab is developing assays to detect COVID-19 viral nucleic acids in swab samples to detect current infections, as well as detect antibodies targeting SARS-CoV-2 in serology samples to determine if someone has been previously exposed and mounted an immune response.

LabKey Open Research Portal for COVID-19 Collaboration

Built using LabKey Server, the LabKey Open Research portal helps CoVen researchers directly coordinate with collaborators to post real-time updates and monitor the progress of ongoing studies. The portal provides a platform that facilitates communication, data uploads, and efficient tracking of updates. These real-time updates allow the CoVen team to fine tune study designs and discuss future directions of studies based on data from each site.

By sharing real-time study updates on the portal, research teams from around the world have accessed the data. This has facilitated further collaboration and helped the CoVen team to learn from other research studies, share and develop standardized clinical scoring criteria, PET/CT imaging techniques, virological and immunological assays, and study designs.

Open Research Portal projects are freely available to researchers. If you are interested in sharing real-time data through the portal, please contact us.

Picking the Right Sample Management System for Your Lab

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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

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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

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[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

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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

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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