Category: About LabKey

What’s New in LabKey 22.3!

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LabKey Server

  • The Text Choice data type provides an easy way to define a set of expected text values for a field. (docs)
  • Sample naming patterns are validated during sample type definition. Example names are visible to users creating new samples. (docs)
  • Queries can be included in published studies. (docs)
  •  Ontology insert and update forms now support type ahead filtering for quick input into ontology lookup fields. (docs)

Sample Manager

  •  Sample Finder: Find samples based on source and parent properties, giving users the flexibility to locate samples based on relationships and lineage details. (docs)
  •  New Storage Editor and Storage Designer roles, allowing admins to assign different users the ability to manage freezer storage and manage sample and assay definitions. (docs)
  •  Redesigned main dashboard featuring storage information and prioritizing what users use most. (docs)

Biologics

  •  ELN Improvements:
    • Notebook entry locking and protection: Users are notified if someone else is already editing a notebook entry and prevented from accidentally overwriting their work.
    • Find notebooks easily based on a variety of filtering criteria. (docs)
  • Freezer Management for Biologics: Create a virtual match of your physical storage system, and then track sample locations, availability, freezer capacities, and more. (docs)
  •  User-defined barcodes can also be included in sample definitions and search-by-barcode results. (docs)

Premium Resources

See the full Release Notes 22.3 (March 2022)

Automating the Instrument-to-Assay Pipeline with the Biologics LIMS and AWS

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Upside foods is a fast-growing start-up working on developing cell-cultured meat for the consumer market. They have a robust R&D pipeline supported by varied teams and processes. Similar to traditional life science organizations, Upside is required to comply with regulatory requests and protocols including those from the FDA and USDA. 

Upside Foods utilize the Biologics LIMS to help answer key questions including:

  • How do various growth conditions affect tissue growth?
  • What combination of production variables produces the best tasting and healthiest cell-cultured meat?  

Answering these questions begins with gathering data in the lab from assays being continuously run by scientists. Prior to LabKey, Upside was using an assay data capture solution consisting of many connected moving parts including spreadsheets, manual processes, data transformations, databases and network drives. This solution was difficult to support and required lots of replication of data that was shaped differently depending on where it was stored. This system lacked:

  • Central management and storage of their data 
  • Audit logging and alerts for each component and the system as a whole
  • Redundancy and disaster recovery
  • Scalability to meet growth needs and increasing R&D complexity 

In selecting the Biologics LIMS, Upside was aiming to keep up with their many changing requirements including new instruments and assays, increasing business logic complexity and the need for a single source of truth for their data. LabKey has a number of ways to capture data including bulk import through the UI. However, Upside wanted to reduce the time and effort it took for uploading data even further, especially from high-throughput assay pipelines. They wanted to make the process as effortless as possible for their scientists. With low latency in getting instrument data loaded in the system, scientists could make faster decisions and trust the data being used for their analyses.

Presented by Jay Kasberger, Senior Manager, Software Engineering at Upside Foods, the video below describes how Upside Foods built a pipeline that leverages AWS to automate the flow of assay data.  By using Lambda and DataSync, Upside Foods reduced the work scientists have to perform to transfer runs and results into the system while keeping thorough logs and automatically alerting to any issues.

Click here to learn more about the Biologics LIMS.

Watch the presentation below:

[vc_video link=”https://www.youtube.com/watch?v=N3sIgSjshx8″]

Veterinary Sample Management at The Ohio State University

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The Ohio State University is using Sample Manager to manage veterinary samples for its influenza monitoring program.

veterinary sample management
Veterinary sample management at The Ohio State University

Presented at the LabKey User Conference, Andrew Bowman, Associate Professor at The Ohio State University shared how his lab is using Sample Manager for veterinary sample management to support a surveillance program monitoring influenza viruses circulating in swine and waterfowl. His presentation provided an overview of the work being done in the lab, their need for a sample management system, benefits they have seen since adopting Sample Manager, and future plans. 

The lab generates more than 10,000 veterinary samples per year and conducts approximately 15,000 tests on these samples annually. The samples being handled by the lab include swabs, environmental samples, serum and PBMC. Projects assigned to the lab have varying data reporting requirements and sample information being captured. As can be expected, one of the major challenges is managing the volume of data and samples.

Prior to Sample Manager, the lab was using an outdated veterinary sample management system based on Filmaker databases. The system was difficult to use and lacked the flexibility needed to adapt to new projects and sample processing requirements. Being an academic lab, there is a continuous turnover of students using the system, creating the need for an easy-to-use application that requires minimal training and IT support.

Sample Manager was chosen as the veterinary sample management system for the following reasons: 

  • Sample Research-focused data management and the flexibility to meet data reporting requirements
  • Sample-centered, alignment with workflow
  • Easily customizable to meet the needs of new projects and assay
  • Intuitive and user friendly- requiring minimal training and support

Some of the key features being used include:

  • The ability to add multiple sources per sample and general flexibility of the system
  • The ease by which new assays can be added and data can be managed/tracked
  • Customer support- LabKey is incredibly responsive and solution-oriented in its approach!

Click Here to learn more and take a tour of Sample Manager!

[vc_video link=”https://youtu.be/BV-isHVUgzU”]

What’s New in LabKey 21.11

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LabKey Server

  •  Cloud: Import folder archives and reload studies from S3 storage. (docs)
  • Specify a custom date parsing pattern. (docs)
  • Subscribe to notifications of changes to specific datasets (docs)
  • Improved visibility options for user-defined queries in the schema browser. (docs)

Sample Manager

  •  Improved interface for managing workflow templates, jobs, and tasks. (docs)
  •  Edit sources and parents of samples in bulk. (docs)
  •  Manage sample statuses like available, consumed, and locked.
  •  Customize the aliquot naming pattern. (docs)
  •  Record the physical location of freezers you manage, making it easier to find samples across distributed sites. (docs)

Biologics

  •  Sample detail pages include information about aliquots and jobs. (docs)
  •  Customize the names of entities in the bioregistry (docs)

Premium Resources Highlights

For the full release notes, click here.

Integrating Benchling Data in LabKey at Inzen Therapeutics

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At Inzen Therapeutics, the data science team uses LabKey Server as a one-stop-shop for data warehousing. Their goal is to help bench scientists quickly answer questions about their data. Through LabKey’s API, Inzen can access previous experiments and run downstream analyses on proteomics and phenotypic assay data. This enables Inzen to better understand the intercellular signals sent during execution of cell death programs, which they have termed “thanokine biology.”

Integrating Benchling Data with the LabKey API

Lab scientists at Inzen use Benchling, a suite of tools used for notebook management, molecular biology, and inventory tracking. It includes its own data warehouse, which contained the sample metadata. However, data scientists at Inzen use LabKey Server for other lab data management functions including storage of all omics data, metadata on measurements, hit lists from previous experiments and curated annotation sets. To help their scientists, Inzen knew they would have to integrate the Benchling data warehouse with LabKey to establish a single source of truth and develop core analytical pipelines. 

Watch the video below to learn how the data science team at Inzen integrated disparate data streams from Benchling and LabKey using the unified LabKey API.

Want to learn more? Request a Demo.

[vc_video link=”https://youtu.be/F4LfvSL4hAw”]

Biomarker Sample Management at Candel Therapeutics

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Candel Therapeutics is using LabKey Sample Manager to manage biomarker samples from the clinical sites where they’ve been collected all the way to the externally performed assays.

At the LabKey User Conference, Jessica Dwyer, Biomarker Operations Manager at Candel Therapeutics, shared how her organization is using LabKey Sample Manager for biomarker sample management. Her presentation covers the process of selecting a sample management software, reasons for choosing sample manager, and how Candel is now using the application. 

Candel is an oncolytic viral therapy company producing therapies to target solid tumors. Their approach to immunotherapy centers on oncolytic viruses that induce immunogenic cell death at the site of injection which then unmasks tumor neoantigens. This process has been shown to create a systemic immune response against tumors with evidence of clinical and biomarker activity demonstrated across several solid tumors. The feasibility and tolerability of this approach has been demonstrated in over 700 patients across multiple phases of trials.

Prior to LabKey Sample Manager, biomarker samples from clinical trials were being tracked using excel spreadsheets. The drawbacks of managing biomarker samples in this way included:

  • Time wasted searching for the latest versions and interpreting data
  • Lack of audit trail and consistency of data between studies
  • Ineffiecient processes for registering and tracking samples

Candel Therapeutics evaluated three different biomarker sample management solutions including Sample Manager. They were looking for software that provided a complete and searchable audit trail, required minimal implementation time and had features that met their needs without work-arounds. After evaluating the options, LabKey Sample Manager was chosen as the solution that most closely matched these requirements. Sample Manager was chosen due to:

  • LabKey’s specialization in the management of clinical trial samples
  • Aliquot features
  • Sample relationship features (data from sample types and sources can be tracked)
  • General ease-of-use 

Watch the video below to learn more about how Candel Therapeutics is using LabKey Sample Manager.

Want to learn more? Request a demo of LabKey Sample Manager!

[vc_video link=”https://youtu.be/YH1ys6VdNdQ”]

The LabKey Biologics ELN at Just-Evotec

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In this panel from the LabKey User Conference, we discuss the roll-out, adoption and impact of the Biologics LIMS Electronic Lab Notebook at Just-Evotec Biologics. Moderated by Bernie Lee, product manager of the LabKey Biologics LIMS, the panelists from Just-Evotec included Tara Kulas, Abigael Brownell and Abby Neumann. These scientists all use the Biologics ELN in their respective functional areas and were critical to the selection and adoption of the Biologics ELN at Just-Evotec. 

Just-Evotec Biologics is an integrated design company focused on technologies to accelerate the development of biotherapeutics while substantially reducing costs. Their mission is to apply these technologies to expand global access to biotherapeutics. LabKey has partnered with Just-Evotec since the inception of LabKey Biologics to shape and refine the capabilities of the product. Tara Kulas led the effort to find a new ELN for Just-Evotec and is the ELN administrator for the organization. You can learn about her work to find the perfect ELN by watching her previous presentation- The Quest for an ELN We Actually Want to Use.

After evaluating many other ELNs in the marketplace, partnering with LabKey emerged as the natural choice since Just-Evotec was already using LabKey Biologics to centralize and manage their data and a trusted partnership had already been established. After gathering requirements, collaborating on design iterations, gathering feedback, and launching an initial release, the Biologics ELN was ready for it’s official rollout at Just-Evotec. 

A few of the highlights shared by the panelists in the video below:

  • The user-friendly design of the ELN helped Just-Evotec quickly adopt the application
  • Easily referencing data and creating templates has led to a significant decrease in the time it takes to author notebooks. 
  • With authoring being less tedious and time-intensive, the quality/completeness of documentation has improved 
  • Collaboration and data sharing has improved and is now more efficient across teams 

Click here to request a demo of the Biologics LIMS.

[vc_video link=”https://www.youtube.com/watch?v=h3ItbNn86Q8″]

Essential Biopharma Software for R&D Data Management

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Biopharma software is an essential tool for managing R&D data of modern biotech organizations. Biologics development is a data-driven endeavor involving many development stages and cross-functional collaboration. The inherent complexity, variety of disciplines producing data, and the sheer volume of data can easily pose a challenge to biopharma research organizations. Many research teams are using general-purpose data management tools (spreadsheets and files) or systems purpose-built for a single data type. This approach can lead to problems in tracking data and duplicating work. This blog post focuses on key considerations when selecting biopharma software for managing R&D data. 

biopharma software

Biopharma data management challenges include:

  • Integrating data generated from disparate scientific specialties
  • Difficulty in finding and highlighting important data (leading to duplication of work)
  • Variabilities in data structure and conventions
  • Lack of visibility into data provenance

These challenges make it difficult for biopharma researchers to answer some basic scientific questions about their data:

  • Do I have the data I need?
  • What is this data? (structured data model, definitions)
  • Where did this data come from? (data provenance, audit history)
  • How and why was it generated? (reproducibility, workflow processes)

Biopharma software can help centralize research data and enforce data standards. This allows for quick and confident answers to the questions scientists ask about their data. Along with data capture, standardizing and monitoring processes is critical to tracking biopharma R&D activity and reducing data inconsistencies.

Biopharma software should include integrated tools for data management.

The LabKey Biologics LIMS provides a central bioregistry with integrated assay data capture, workflow management, and a “data-connected” electronic lab notebook. We consider these to be the pillars of a comprehensive biopharma software solution for data management.

Bioregistry

A bioregistry helps scientists define, register, and review interconnected biological entities and their samples. By centralizing biopharma R&D data, researchers can easily find, view, and navigate through entities, their lineage, and data relationships. For example, using a bioregistry, scientists can easily find a specific molecule and see all the related sequences, samples containing it, and related assay data.

Assay Data Management

Assay data is the decision-making criteria for discovery, process development, and quality. It is generated by all contributing teams and its relevance endures throughout. Having a central, structured, and workflow-related assay data capture mechanism is essential for streamlining decision making, hand-offs, and post hoc analysis. It ensures that consistent data structures are used throughout the biopharma development process, sets expectations for needed data, and makes clear where critical data can be found.

Electronic Lab Notebook

An ELN is designed to help scientists efficiently organize and document their ongoing research. A data-connected ELN provides even more value by having access to the bioregistry, assay, and sample data captured so that additional work is not required to find and include it. This integration paradigm maintains data integrity while enabling easy data exploration and collaboration.

Workflow Management

Defining collaborative biopharma workflows helps set expectations for contributors and managers. It supports the fulfillment of material and data needs and prepares the way for process optimization, scheduling, and cross-team alignment. These workflow tools facilitate strategic experimentation, simpler data hand-off, and easier planning.

Biologics LIMS- Biopharma R&D software designed for efficient data management.

Biologics LIMS is a powerful suite of integrated tools to help scientists manage biologics research data, improve lab processes, and collaborate efficiently. The software provides biopharma researchers with streamlined registration and tracking of biological entities and samples in a central bioregistry. The bioregistry is seamlessly integrated with tools for workflow management, assay data management, and an electronic lab notebook (ELN). This combination of software tools forms a cohesive application that serves as a central hub for managing biotherapeutic development data, processes, lab notebooks, and collaboration efforts.

LabKey Biologics helps scientists:

  • Speed up decision-making with unified ELN, bioregistry, workflow, and assay data management tools
  • Centralize and connect data for a holistic view of your data landscape and interrelationships
  • Manage and optimize lab processes with a workflow tool designed for biopharma R&D

Click here to learn more about LabKey Biologics and take a product tour.

Scientific Collaboration with LabKey Sample Manager

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Many researchers are continuously seeking ways to boost scientific collaboration. As with other disciplines, enabling scientific collaboration requires the right tools and processes. This is especially true when researchers are sharing samples that need to be tracked at each step of their lifecycle. For some labs, collaborative sample tracking involves a piecemeal approach of emails, spreadsheets, and whiteboards to give teams some visibility into the next steps, assigned work and upcoming projects. This method of sample tracking is highly prone to error and can easily get unwieldy as a lab grows or the complexity of sample processing increases. 

Finding a sample management software that tracks samples throughout their life cycle while also enabling scientific collaboration is imperative for the modern laboratory. Sample Manager has been designed by scientists, for scientists, to help get work done in the lab. We have created a tool that integrates sample registration, storage, experimental data and work assignment for doing all your sample-related work in a single application. Below are a few features that help enable scientific collaboration in the lab.

Workflow Management for Scientific Collaboration

Our task-based lab workflow management tool allows teams to capture the exact work that needs to be performed on samples. Using customizable templates, labs can easily standardize processes and create workflows that accurately reflect their SOPs. Common lab processes like sample receipt, shipping preparation, processing, and assay requests can all be managed using the Sample Manager workflow tool. For each workflow, samples are selected for inclusion in the job, tasks are assigned to individual team members, and notifications communicating the status are sent. The ability to set due dates and the priority of the work allows teams to plan and prioritize work appropriately. 

Freezer Management/Sample Location Tracking

Our sample-centric freezer management tool gives teams insight into freezer capacity and the physical storage of samples. Team members efficiently work in an intuitively designed virtual freezer environment, capturing notes for freeze/thaws and displaying those in the Sample Timeline. Users can quickly understand storage capacity, relative sample breakdown, and overall sample status across storage units in the lab.

Picklists

Teams can create private or public Picklists of samples to generate pull lists, manifests or any other type of list that would be useful for tracking and sharing samples. Sharing picklists with team members enables visibility into user-curated lists of samples and reduces the need for exporting, printing and emailing lists of samples to team members. Shared Picklists can be used to print labels, check samples in and out storage, and add samples to workflow jobs. 

Click here to learn more about Sample Manager and take a tour!

What’s New in LabKey 21.7

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LabKey Server

  •  File Watchers – Use file watchers to automate the import of sample and assay data.
  •  Ontology Concept Picker – Improve data entry by guiding users to a specific part of the concept hierarchy.

Sample Manager

  •  Study/Sample Integration – Add samples to studies and associate them with specific participants and timepoints.
  •  Aliquots – Create aliquots of samples singly or in bulk.
  •  Picklists – Create and manage picklists of samples to simplify operations on groups of samples.
  •  Move Storage Units – Track movement of storage units within a freezer, or to another freezer.
  •  Barcode/UniqueID Fields – A new field type, “UniqueID”, generates values when samples are added to a Sample Type or when the barcode field is added to an existing sample type.

Biologics

  •  Electronic Lab Notebooks have been added to LabKey Biologics. Link directly to data in the registry and collaboratively author/review notebooks.
  •  Hide Sequence Fields – Nucleotide and Protein Sequence values can be hidden from users who otherwise have access to read data in the system.

Premium Resources Highlights

Click here to read the full 21.7 Release Notes