Tag: About LabKey

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

•  Premium Resource: Change the Encryption Key
•  Premium Resource: LabKey Data Finder: The DataFinder module has been enhanced to support partial word searching, custom publication facets and reordering of facets, and multiple data finders on a single server.

See the full Release Notes 22.3 (March 2022)

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

•  Premium Resource: Download a File with Python
•  Premium Resource: LabKey Data Finder
•  Premium Resource: Show Calculated Columns in Other Queries

For the full release notes, click here.

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

•  Integration with BarTender – Print BarTender labels and barcodes for samples in 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

•  Ontology Module – Import and manage standardized vocabularies. A new data type “Ontology Lookups” applies ontology concepts to your data.
•  Query-based Specimen Import – Automatically load specimens from a Query specified on the server.
• NAb Assay – Improved Curve Plotting – NAb dilution data is now exported with fit parameter data, simplifying full curve plotting
• Field Editor Export/Import – Export and import sets of fields to reuse common data columns.

Premium Resources Highlights

•  Premium Resource: Plotly Dash Demo – Example scripts for using Plotly Dash.
•  Premium Resource: Add a Custom Security Role – Developers can define a custom security role in a Java module.
•  Premium Resource: Server Encoding – Ensure correct HTML encoding.

Community Highlights

• Watch Sessions from the LabKey User Conference 2020

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

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]

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!

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

In early June, LabKey held two European User Conference events bringing together users in Basel, Switzerland and London, UK. Attendees had the opportunity to share their success stories and learn about the multitude of ways that LabKey could assist in their research efforts. Experts from LabKey led training sessions and gathered user feedback on upcoming development projects including our soon to be launched Sample Management solution. If you missed it, here’s a brief recap and we hope you will join us next time!

Using LabKey to Enable Reproducible Research

Dr. Thomas Schlitt, Staff Scientist, presented how the Department of Cognitive and Molecular Neurosciences at the University of Basel uses LabKey to gather and analyse data collected from volunteers taking part in psychological research. The data collected includes results of memory tests, picture recognition tasks, and reports on adverse events and medication taken during research studies. These diverse datasets are brought together using templates of lists and scripts to enable efficient adaptations in new studies.

A Wayfarer’s Guide to the Galaxy of LabKey inside the NIHR Oxford Biomedical Research Centre

Oliver Freeman, Technical Architect, discussed a few ways LabKey’s deployment inside the National Institute of Health Research (NIHR) Oxford Biomedical Research Centre is aiding research. One of their LabKey projects is a data collection tool for the Hepatology Research Project, a study with a custom-built UI utilizing Extract-Transform-Load processes (ETLs). LabKey is also used in the NIHR HIC Hepatitis Project to allow submission of files into the collation system, followed by the viewing and querying of the collated data. In the future, they will deploy a portal for clinical research data products across the organization employing native LabKey features including the metadata catalogue, project and folder level security, and LDAP authentication to control who has access to the data.

Genomic Research of Diagnostics of Rare Diseases using LabKey

Dr. Jean-Baptiste Rivière, Assistant Professor, described how the McGill University Health Centre (MUHC) and its Research Institute (RI-MUHC) is using LabKey Server to manage the explosion in data production triggered by the movement of genomic technologies from research to broad use for etiologic diagnosis of patients. They rely on the flexibility and robustness of the LabKey platform as they collect, standardize, integrate, and share diverse health and laboratory data on rare diseases and cancer. Specific uses include web-based test requisition forms and questionnaires, tracking of biological specimens and laboratory results, and generation of bilingual clinical reports of molecular results.

[vc_column width=”1/6″][vc_column width=”2/3″][vc_cta h2=”Join Us in Seattle this Fall” add_button=”bottom” btn_title=”Learn More and Register” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_align=”left” btn_link=”url:http%3A%2F%2Fwww.labkey.com%2Fproduct%2F2019-labkey-user-conference-workshop%2F|title:2019%20LabKey%20User%20Conference%20%26%20Workshop%20%7C%20Seattle%2C%20WA||”]The next LabKey User Conference will be held in Seattle October 3-4, 2019, bringing you more great presentations and opportunities to connect with the LabKey community. Hope to see you there![/vc_cta][vc_column width=”1/6″]

LabKey Server helps research teams efficiently manage, analyze, and publish biomedical research data at scale, maximizing its value. To learn about other applications of LabKey Server, check out more user presentations, or contact us.

Long-time partners of LabKey know our story well; born out of Fred Hutch, the LabKey platform was developed to help research teams make sense of the large volumes of research data being generated by high-throughput proteomics analysis techniques.

While our mission is still the same, the platform has greatly expanded over the last 13 years to support new data types, analysis methods, and research disciplines from rare disease investigation to large-molecule drug development. In their recent article, GeekWire highlights LabKey’s evolution from a 3-person team in a Fred Hutch office to the self-sustaining solutions provider we are today.

LabKey’s motivation hasn’t changed a bit. “Every one of our customers you would want to be wildly successful,” said [LabKey CEO,] Michael Gersch. “Because they’re helping humanity. That’s what’s so neat about what we get to do.”

Read the full article on GeekWire.com to learn more about the history of LabKey and our vision for what’s next.

Original Article
Thorne, James. “How Fred Hutch spinout LabKey bootstrapped its way to compete in health care’s big data.” GeekWire, December 28, 2018, https://www.geekwire.com/2018/fred-hutch-spinout-labkey-bootstrapped-way-compete-health-cares-big-data/