Category: About LabKey

Sample Manager unveils freezer management features to help labs track and organize samples.

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Freezer management systemLabKey has launched a comprehensive solution for managing laboratory freezer storage and sample locations within its user-friendly sample management software- LabKey Sample Manager.

By including robust freezer management capabilities in a full-featured sample tracking and workflow management system, LabKey Sample Manager aims to serve as a collaborative hub for sample processing work in the laboratory. The application helps standardize and guide lab processes while capturing the entire history and chain of custody for each sample. The addition of freezer management integrates the tracking of sample locations, freezer storage, sample volume, and freeze/thaw counts into an already rich feature set for managing sample processing work.

“Having worked in the lab for more than ten years, I can attest to the need for integrated sample and freezer management software that is flexible and easy to use. I’m excited that with LabKey Sample Manager, we have created just that” says Hannah Brakke, Product Manager at LabKey. “We have developed a truly intuitive application that allows laboratories to register and track their samples and collaborate- all in one place. Adding a straightforward freezer management system with a modern user interface takes the sample tracking capabilities to the next level.”

Sample Manager gives laboratories the power to use the freezer management features in a way that matches their lab and workflow requirements by taking a “sample-centric” approach. This allows samples and their data to live in the system before a sample has been stored in the freezer and even after they have been removed from storage in the lab. Using this approach to freezer management, Sample Manager helps to streamline lab workflows and takes into account the real-world sample management operations of busy labs. Additionally, the flexibility of Sample Manager allows users to configure the application to exactly match the physical freezer storage options in their lab.

LabKey Sample Manager Overview

LabKey Sample Manager is a flexible and intuitive application designed to boost lab efficiency and productivity. Easily track samples, manage freezer storage, create workflows, and unify samples with experiment data. Use the links below to learn more about LabKey Sample Manager:

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

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

Three Reasons Freezer Management Software is Vital

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If you’ve worked in a lab, you’ve likely used some form of freezer management to manage your sample storage. For some labs, this may simply be a paper lab notebook where freezers, boxes, and sample locations are annotated. Others may periodically update an Excel file with samples stored in the freezer and place a print out of the spreadsheet on the freezer itself. However, for truly efficient and organized labs, nothing beats having freezer management software to manage your freezer capacity and sample inventory. Below are 3 key reasons why you need software to manage your lab freezer storage. 

1. Your samples are precious and should be treated that way.

Samples can be one of the most precious things in the lab, sometimes they are even irreplaceable. The time spent collecting, processing, and collecting data from samples means they are valuable not only to your research but also to the cost efficiency of your lab. Misplacing and looking for lost samples can be a huge waste of time for laboratory staff and even more so if the samples are never found. Using freezer management software ensures that your freezers are kept organized and reduces the chances that you will misplace valuable samples.

2. Excel and paper-based freezer management can’t keep up with busy labs.

Although Excel and paper-based systems may be able to keep up with the needs of a very small lab, they are very difficult to keep updated with accurate information and definitely don’t meet the needs of larger or growing labs. Busy staff in the lab will need to manually/visually judge freezer capacity, update multiple sheets and samples when making simple changes, and have to manually keep track of sample volumes and freeze/thaw counts. This method of freezer management is highly prone to errors from day-to-day use not to mention during scheduled clean-outs and organization of the freezer.

3. Complete and accurate auditing is nearly impossible without freezer management software.

Auditing and organizing your samples is a much easier task with freezer management software.  You’ll have a full record of all check-in/check-out events for samples, by which staff, and a full history of the location and movement of samples in the freezer. This level of completeness and accuracy is much more difficult to achieve using paper or excel. Freezer management software captures all of the information you need for a comprehensive audit of your freezer storage and samples. 

Freezer Management with LabKey Sample Manager

With Sample Manager, we have introduced a sample-centric freezer management solution into the application. This means you can create samples, add metadata and lineage information, perform work and even upload assay data — all without having to use the freezer management tool. Of course, if you plan to store your samples, freezer management is there to help by:

  • Managing your freezer with an end-to-end sample tracking system that stores the entire sample history and chain of custody in one place
  • Providing a customizable, flexible structure to accurately reflects the physical freezers in your lab
  • Tracking samples in and out of the freezer (freeze/thaw counts) and automatically calculating and tracking sample volumes 
  • Helping you to easily find samples in the freezer and move samples between freezers
  • Tracking and maintaining full audit logs of the freezer and of the samples

The best way to encourage users to adopt a new system is by providing them with benefits that actually help them- save them time, make tasks simpler, etc. Additionally, when a system becomes the primary source of truth for team members, it becomes easier to adopt because that’s where the information lies. Click here to learn more about our freezer management solution. 

What’s New in LabKey Server 20.11

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We are excited to announce our 20.11 release! This release includes major updates to Sample Manager, Biologics and LabKey Server.  See the full release notes, and highlights below.

Sample Manager

Biologics

  •  Sample Management – Improved user experience for defining and importing samples, and generating sample IDs, including importing samples by drag-and-drop and directly entering sample information in the user interface.

LabKey Server

Premium Resources Highlights

Community Highlights

See the full release notes: Release Notes 20.11 (November 2011)

Managing ELISA and ELISpot Data with LabKey Server SDMS

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High throughput plate-based immunoassays such as ELISA and ELISpot are important tools in drug discovery, clinical trials, bioanalytical labs and immunological research. With the advancement of these assays into microplates and their relatively inexpensive nature, both of these assays are widely used globally to evaluate immune responses to a variety of antigens.

Because of their low price point and technology requirements, ELISA and ELISpot assays are often performed in a high-throughput manner which produces a large amount of data in a short time frame. To support the reproducibility of experiment results, teams need lab data management tools that are scalable enough to manage this high volume data in a controlled manner without causing research bottlenecks. LabKey Server provides support for efficient ELISA and ELISpot data management by:

Streamlining Data Management in the Laboratory

LabKey Server helps streamline the management of immunoassay and other laboratory data by:

  • Automatically importing instrument files upon availability using LabKey file watchers
  • Providing automated cleaning, validation, and transformation of data from laboratory instruments, databases and software
  • Structuring experiment results in data grids that can easily be sorted, filtered, and queried

Tracking Data Provenance

LabKey provides scientists with mechanisms for capturing data provenance by:

  • Offering users easy-to-understand graphical plate mapping tools
  • Allowing users to add metadata about the antigen or immune-responder
  • Providing the ability to calculate background and normalize data when appropriate
  • Visualizing calibration curves or normalized spot counts for dependable analysis

Facilitating Lab Data Integration & Analysis

LabKey helps scientists integrate, analyze and share their ELISA and ELISpot data by:

  • Allowing users to easily integrate their plate-based data with other related data
  • Providing built-in visualization tools for live or snapshotted analyses
  • Offering a mature permissions strategy for securely sharing data and analyses with collaborators

LabKey Server helps research teams efficiently manage lab data at scale.


Click here to request a demo.

Multi-Attribute Method reporting with Panorama and Skyline

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Panorama is a web-based data management system for targeted mass spectrometry data that integrates closely with Skyline.

The Multi-Attribute Method (MAM) is designed for improved simultaneous detection, identification, quantitation, and quality control (monitoring) of molecular attributes. Panorama has recently added MAM-specific reporting to its existing set of analytics, offering immediate results and data sharing to any imported data. Additionally, Panorama and AutoQC’s automated workflow provide longitudinal tracking of MAM-related metrics for QC purposes.

Results:  Skyline lets users easily set up the proteins and peptides to analyze, and pull in raw data from all of the major mass spec vendors without needing to do a separate conversion step.  Panorama organizes data into folders, and offers different folder types that are optimized for different workflows and analyses. A new MAM folder type introduces predefined reports, including a Peptide map report and a Post-translational modification report which shows the proportion for each peptide variant’s peak area across samples. More MAM-focused reporting is being added, and at any time, data can be pulled into Spotfire, Tableau, or R for additional visualization.

Conclusions: Groups first started creating MAM-related reports in Panorama via custom SQL queries in 2015, but these were not built-in as standard reports or widely distributed. As interest in MAM has grown, the Panorama team saw the need to generalize them and make them broadly available. The initial set of reports include post-translational modification percent and peptide map reports. A collaboration between users and the Skyline and Panorama development teams resulted in new capabilities to override how peptides and their variants are grouped when calculating the percentage that each variant represents of the whole. This flexible approach means that users can either use the default, which groups all PTM variants together, or group based on sequence variants or other factors. Supporting these reports directly also means that database schema changes and precalculation can speed up query times by 20x or more. Additionally, because Panorama can track a wide variety of data for automated longitudinal tracking, these MAM-related metrics can be easily incorporated into QC folders where they can be analyzed with statistical process control techniques like Levey-Jennings, CUSUM, and moving range plots. As of January 2020, more than 400 labs are using Panorama projects free of charge to manage targeted mass spectrometry assays on http://panoramaweb.org/, a server hosted by the MacCoss lab at the University of Washington. Additionally, major pharmaceutical companies and other organizations have deployed their own in-house installations of Panorama.

Panorama Partners Program

The Panorama Partners Program accelerates the adoption and integration of Panorama into member organizations’ targeted mass spectrometry workflows. Partners work directly with the Panorama and Skyline development teams, help shape the direction of ongoing development, and receive exclusive premium features.

Watch the daily sessions from the 2020 LabKey User Conference!

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The 2020 LabKey User Conference featured informative sessions showing how LabKey is being used by a variety of life science research organizations, as well as educational talks from the LabKey Team. Conference highlights include:

  • Watch presentations from NIAID/NIH, Nestlé Research, Just-Evotec Biologics, and Knight Cancer Institute showing how they have partnered with LabKey
  • See previews of our upcoming Biologics Electronic Lab Notebook (Day 2), and our Freezer Management solution within LabKey Sample Manager (Day 3)
  • Hear about LabKey MyStudies (Day 4)- an open-source system for conducting IRB-approved clinical trials, collecting patient reported outcomes, and obtaining informed consent using mobile devices
  • Learn from our developers with our Tech Talks (Day 4) to get a deep dive into more technical areas of the platform

[vc_custom_heading text=”Have questions? Want more information?” font_container=”tag:h2|text_align:center” use_theme_fonts=”yes”][vc_btn title=”Contact Us” color=”green” align=”center” link=”url:https%3A%2F%2Fwww.labkey.com%2Fabout%2Fcontact%2F”][vc_separator][vc_row equal_height=”yes”][vc_custom_heading text=”Day 1, October 6th” use_theme_fonts=”yes”][vc_video link=”https://youtu.be/HiT_CLKG7Bs”][vc_btn title=”Watch on YouTube” color=”green” align=”left” link=”url:https%3A%2F%2Fyoutu.be%2FHiT_CLKG7Bs”]Introduction
Presented by Michael Gersch, CEO, LabKey

00:11:55 – LabKey Server Product Update
Presented by Adam Rauch, VP of Product Strategy, LabKey

00:28:27 – HGRepo Informatics Framework for the NIAID/DIR COVID-19 Immune Response Consortium
Presented by Sandhya Xirasagar Ph.D., Lead, Clinical and Laboratory Informatics Section, NIAID & Jason Barnett, Contract Lead, Medical Science and Computing, Inc. 

00:54:35 – Assay and Study Management with LabKey Server
Presented by Bernhard Sonderegger Ph.D., Senior Specialist Data Systems and Management, Nestlé Research

01:15:00 – Reporting and Visualizations via ODBC Integrations
Robert Morphew, Technical Program Manager, LabKey[vc_separator][vc_row equal_height=”yes”][vc_custom_heading text=”Day 2, October 7th” use_theme_fonts=”yes”][vc_video link=”https://youtu.be/_0j5TTzB1NI”][vc_btn title=”Watch on YouTube” color=”green” align=”left” link=”url:https%3A%2F%2Fyoutu.be%2F_0j5TTzB1NI”]LabKey Biologics Update
Presented by Bernie Lee, Product Manager,  LabKey

00:28:52 – ELN (Electronic Lab Notebook) Preview
Presented by Bernie Lee, Product Manager, LabKey

00:56:54 – The Quest for an ELN We Actually Want To Use
Presented by Tara Kulas, Scientist, Analytical Sciences, Just – Evotec Biologics

01:26:38 – Introduction to Panorama and LabKey Support for Targeted Mass Spectrometry
Presented by Josh Eckels, VP of Engineering, LabKey[vc_separator][vc_row equal_height=”yes”][vc_custom_heading text=”Day 3, October 8th” use_theme_fonts=”yes”][vc_video link=”https://youtu.be/bolH_k0YQq0″][vc_btn title=”Watch on YouTube” color=”green” align=”left” link=”url:https%3A%2F%2Fyoutu.be%2FbolH_k0YQq0″]LabKey Sample Manager Update
Presented by Hannah Brakke, Product Manager, LabKey

00:26:09 – Freezer Management Preview
Presented by Hannah Brakke, Product Manager, LabKey

00:57:02 – Data Management in Precision Oncology
Presented by Patrick Leyshock, Ph.D., Knight Cancer Institute, Oregon Health & Science University

01:27:20 – Using LabKey Server with Sample Manager
Presented by Steve Hanson, Director of User Education, LabKey[vc_separator][vc_row equal_height=”yes”][vc_custom_heading text=”Day 4, October 9th” use_theme_fonts=”yes”][vc_video link=”https://youtu.be/ikEeVwjPa24″][vc_btn title=”Watch on YouTube” color=”green” align=”left” link=”url:https%3A%2F%2Fyoutu.be%2FikEeVwjPa24″]LabKey MyStudies: Supporting Mobile E-Consent, Study Design and Infrastructure for Clinical Trials
Presented by Adam Rauch, VP of Product Strategy, LabKey

00:30:26 – Automate Data Import and Processing using File Watchers
Karl Lum, VP of Engineering, LabKey

01:00:26 – Using LabKey Artifacts for your Build Process
Presented by Susan Hert, LabKey

01:28:53 – JavaScript Development within LabKey Server
Presented by Nick Kerr, LabKey

01:59:39 – Bringing Your Data Together
Presented by Binal Patel, LabKey

02:30:19 – LabKey Cloud Hosting and Best Practices
Presented by Stuart MacDonald and Isa Farnik, LabKey[vc_separator]

Browse the Human Immune System with HIPC’s ImmuneSpace Powered by LabKey

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Browse Human Immune System Data

The Human Immunology Project Consortium (HIPC) program was established by the NIAID Division of Allergy, Immunology, and Transplantation (DAIT) as part of the overall NIAID focus on human immunology. To support the data management, analysis, and research efforts of HIPC, ImmuneSpace was developed. This project is led by Dr. Gottardo of the Fred Hutchinson Cancer Research Center. 

Immune system related data, collected from over 100 studies at HIPC research centers, is available to the public in ImmuneSpace, developed in collaboration with LabKey. Well-characterized human cohorts are studied using a wide variety of tools including:

  • Multiplex transcriptional, cytokine, and proteomic assays
  • Multiparameter phenotyping of leukocyte subsets
  • Assessment of leukocyte functional status

LabKey Server Support for HIPC

LabKey Server provides the underlying system to centralize data for securely publishing, aligning, and harmonizing datasets across what would otherwise be siloed study repositories. Shared datasets and extensible schemas help bring diverse data together in a way that it can be treated as a global data bank.

The research network data centralization solution offered by LabKey server is specifically designed to: 

  • Bring together data from disparate studies, making the data centrally available 
  • Align data structures to minimize manual processing and facilitate integration
  • Provide quality control tools to validate and standardize data from contributors
  • Create secure workspaces to curate data prior to sharing with a wider audience
  • Facilitate exploration and analysis of of complete integrated datasets
  • Visualize, analyze, and report on aggregated data using built-in plotting and reporting tools. For example, LabKey Server’s powerful integration with the R statistical programming environment supports presenting R script results as live reports within LabKey Server.

Explore the new HIPC Interface

The ImmuneSpace platform recently launched a new Data Finder interface which makes it easy for users to explore and analyze datasets from hundreds of studies. Developed in ReactJS, with consulting support from LabKey developers and designers, plus extensions to the APIs, this modern interface presents an intuitive browsing experience. LabKey’s integrations with analysis and visualization tools including RStudio help power unique solutions like the ImmuneSpace DataFinder. 

Filter by patient characteristics, study focus, and even by the type and timeframe of data available. Dashboard graphics update in real time to guide you as you make selections.

HIPC Data

Identify your own cross-study participant group of interest and save it for deeper analysis.  Use the group as a basis for visualizations and analysis.

Investigating hypotheses across this existing landscape of collected data can unlock new insights for future study and help you connect with research similar to your own. Filtered study details can be scanned in a card format, or sorted in any way you choose.

Click Here to get started by registering for a free account.

FDA releases COVID MyStudies with support from Harvard Pilgrim Healthcare Institute and LabKey

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Previously released as FDA MyStudies, COVID MyStudies is now available as a free platform to assist investigators in remotely and securely obtaining informed consent from patients for eligible clinical trials when face-to-face contact is not possible due to COVID-19 control measures.

COVID MyStudies

“The agency is providing this resource after hearing that investigators were having difficulties obtaining informed consent for clinical trials when patients were in isolation rooms in health care facilities or could not travel to outpatient clinics,” noted the FDA. By obtaining consent from patients remotely, COVID MyStudies can help ensure that clinical trials related to COVID-19 are not unnecessarily delayed.

COVID MyStudies is available on the Apple App and Google Play stores. 

Before using the app, investigators must contact the FDA. If a pre-IND or IND number is available, it should be included in the preliminary contact email. Investigators will provide their informed consent documents to the COVID MyStudies team to be added to the app. They will then have a chance to review all informed consent documentation within the app before incorporating it into their trials.

LabKey for COVID MyStudies

Harvard Pilgrim Health Care Institute (HPHCI) was selected by the FDA to lead the development of the FDA MyStudies mobile app. HPHCI in turn selected LabKey Server as the supporting data management solution and Boston Technology Corporation (BTC) as the developer of the mobile interface.

The flexible architecture of LabKey Server and its ability to handle PHI/PII data in a manner compliant with HIPAA and FISMA regulations leant itself well to the COVID MyStudies project. The Registration Server utilized to manage electronic consent, authentication, preferences, and notifications, is built upon the LabKey Server platform.  LabKey also provided the HIPAA/FISMA hosting environment for the application. You can learn more about how LabKey supported the FDA MyStudies app by reading our case study.

Related Resources

COVID MyStudies Support Documentation – LabKey

COVID MyStudies Announcement – FDA

Contact the support team at FDAMyStudiesContact@harvardpilgrim.org

Contact FDA at CDERMedicalPolicy-RealWorldEvidence@fda.gov

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)