Category: About LabKey

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

What’s New in LabKey Server 20.3

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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.

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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

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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

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[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

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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

Our Commitment to Data Security

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Since our inception in 2003, security has been of the utmost importance to LabKey and our research partners. We take a proactive approach to improving the platform to overcome the ever-evolving cyber security challenges faced by companies in every industry. 

At LabKey, security begins with educating our developers on avoiding security vulnerabilities through proper coding and best practices. Every feature is designed with security in mind, ensuring that only authorized users are able to view and modify data. Each release of LabKey Server undergoes extensive automated and manual testing to identify potential bugs and vulnerabilities before release. Additionally, we employ automated security scanners and regularly use independent cyber security firms to perform manual penetration testing of the platform. Detailed reports from these efforts are reviewed and any issues are quickly fixed. 

Recently Added Security Features

LabKey releases three major versions of the LabKey Server platform each year followed by subsequent maintenance releases. We encourage our users to always update to the most current release of LabKey Server to ensure they have the maximum protection against security risks. Below are just a few security features included in recent releases. 

Cross-Site Request Forgery (CSRF) Protection – Beginning with version 19.1, LabKey Server enforces CSRF protection (requiring verification of a CSRF token) on all POST requests and, as of 19.3, it will detect all mutating operations and block them if they are attempted outside of a CSRF-protected POST request. For more information on CSRF attacks, click here.

External Redirects Whitelist – LabKey Server restricts the host names that can be used in parameters that provide redirect URLs. By default, only redirects to the same LabKey instance are allowed. Other server host names must be whitelisted by administrator to allow them to be automatically redirected. For more information on unvalidated redirects, click here.

Antivirus Scanning (premium feature) – File uploads, attachments, archives and other content imported through the pipeline or webdav can now be scanned for viruses using ClamAV. 

Vulnerability Management & Resolution

On rare occasions, we may identify or be notified of an issue that poses a security risk. When this occurs, the LabKey team promptly assesses the issue and determines a timeline for resolution based on the severity of the risk. After our initial assessment, we fix the identified vulnerabilities and deliver maintenance releases of the latest production version to our clients as soon as possible. Maintenance releases are also delivered for critical security issues and high priority bug fixes in older production versions of LabKey Server that are still in active use.

To download the most recent version of LabKey Server, click here.

Benefits of Unifying Lab Samples with Assay Data

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Many laboratories experience challenges with their sample data management functions. Samples, aliquots of samples, and the data derived from them are often stored as a mixture of paper and electronic records, or in hard-to-search electronic laboratory notebooks. Difficulty in managing complex interlinkages and the inability to tie results data back to sample records can cause duplicate assays to be performed and puts data integrity at risk. Having a system that unifies assay data directly with sample information provides bench scientists, lab managers and investigators with a comprehensive view of the work that has been, or needs to be performed in the lab. It also provides downstream researchers with valuable information on how and when results were derived for each sample.

By unifying your lab samples with assay data, you can:

  1. Analyze, interpret and report the data more accurately. With an understanding of how samples were generated and pre-processed, scientists can ensure their downstream data analysis takes these sample metadata into account when they perform their analysis. This improved reproducibility in the lab and generates publication-ready data.
  2. Easily attain accurate insight into what data has been collected around a given sample, avoiding the time consuming process of searching through lab notebooks or loose data files. Knowing what data has been generated will reduce duplicative experiments, increase productivity and ultimately result in less overhead expenses.
  3. Generate data provenance between data that is created from samples, allowing users and auditors to easily understand how data was generated.

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 integration of various types of tabular assay data with samples and their corresponding metadata. This provides a complete picture of ongoing experiments and data collected. Additionally, Sample Manager allows laboratory staff to easily capture sample lineage and assign samples to customizable laboratory workflows.

Contact Us for more information regarding Sample Manager.

Learning and Networking at the LabKey User Conference 2019

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The annual LabKey User Conference was held in Seattle on October 3rd and 4th. As with every LabKey User Conference, the event provided LabKey users the opportunity to connect with other researchers and developers as well as learn directly from the LabKey team. Through user presentations, technical talks, discussion groups and networking sessions, attendees expanded their knowledge of the LabKey platform and learned how LabKey is solving data integration, collaboration and workflow challenges faced by other organizations.

For the LabKey team, the User Conference is a wonderful opportunity to learn from our users. The LabKey Server platform, Biologics and our upcoming Sample Manager application have all been developed with significant input and guidance from the scientific research community. As we develop LabKey solutions, this input continues to be the guide by which we prioritize features, integrations, UX decisions and more.

This year’s LabKey User Conference was filled with insightful contributions from speakers and valuable workshops and guidance from the LabKey team. Below are just a few highlights of presentations at the conference. In the coming weeks, we will be sharing some of the exciting presentations from our users and developers. To view this year’s conference program with full abstracts, click here.

LabKey User Presentations

“A Wayfarer’s Guide to the Galaxy of LabKey inside the NIHR Oxford Biomedical Research Center”
Oliver Freeman – Oxford Biomedical Research Centre Clinical Informatics Group, University of Oxford 

“Mapping Cell Line Development Workflows with LabKey Biologics”
Bo Zhai, Cell & Developability Science, Janssen Research & Development

“LabKey for Multicenter R&D on Biofuels and Bio-based Products”
James R Collett, Chemical and Biological Process Development Group, Pacific Northwest National Laboratory (PNNL)

“LabKey and ORIEN Informatics at City of Hope”
Vincent La, City of Hope

“Molding and Maximizing the LabKey Platform for Clinical Translational Research”
Anthony Corbett, Research Data Integration and Analytics Group, University of Rochester Medical Center

LabKey Tech Talks

ReactJS Development: Getting Started
Best practices for building ReactJS based applications with LabKey. Development tips and tricks, practical examples, and advice for developers.

Sample Lineage
Learn how Sample Derivation works in LabKey Server. Explore underlying data structures and use of APIs. See how to access lineage in LabKey.

Visualizing LabKey Data
An overview of how external integrations expand your options for creating reports and visualizations. See how to present LabKey data using Tableau, Spotfire, Matlab, Shiny and more!

LabKey Development Process
Learn about the internal LabKey development process. Covers feature branch workflow, pull requests, test automation, formal and patch releases, and other things external developers need to know.

Quality Control with LabKey Server
Explore strategies for quality control and reporting within LabKey Server and Biologics. Learn to incorporate QC trend reporting, automatic QC options during import, and setting of QC states into your workflows.

Thank you to all who attended and contributed to a valuable and insightful LabKey User Conference!

For the full conference program – click here

Tableau Integration with LabKey for Research Data Visualizations

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More than a tool to facilitate data integration and analyses, LabKey has partnered with Tableau to help research teams visually communicate their findings and build consensus with stakeholders. After all, the most important scientific discovery can’t change the world unless it can get your attention. Key insights gleaned from complex biomedical research data can be overwhelming to explain and even more difficult for some audiences to understand. Insightful and beautiful visualizations created in Tableau from data within LabKey Server can help bring complex data to life, and clearly communicate key results.

Seamless Integration of LabKey Data with Tableau

LabKey integrates scientific data with a wide variety of external analysis and presentation tools, including Tableau Desktop. Gone is the need to hand over research data to visual designers who may not understand the science. The LabKey integration with Tableau allows you to make compelling charts and plots with tools designed for analysis. With Tableau and LabKey together, you can easily create compelling graphs, tables  and other visualizations from your own research data. Presentations can be “live” so they automatically update when additional data is incorporated, or if you prefer, your research data visualizations can reflect a static snapshot.

Tableau Technology Partner 

As a Tableau Technology Partner, LabKey adds the ability to connect biomedical  research data to the analytics and visualizations available with Tableau. Drag and drop the data you want, customize colors, styles, and layouts, and never pause or lose the integrity of your ongoing research. Tableau partners with leading technology companies in the data and analytics industry to seamlessly integrate with Tableau so people can collect, store, transform and connect to the data that is important to them.

Video: Using Tableau to Visualize Data in LabKey Server

Read more here:

https://www.labkey.org/wiki/Documentation/page.view?name=tableau