Category: About LabKey

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

Custom LIMS Software for Engineered Mini-Proteins

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Optide-Hunter

Scorpion venom can kill you, but there is a lot to learn from it. Keeping the part of the molecule that crosses the blood brain barrier and attaching a specifically targeted therapy for treating brain tumors is being made possible by the Olson Lab at Fred Hutch with the help of a custom LIMS software developed on LabKey Server.

The engineering of protein-based therapeutics is a complicated but promising strategy for improving treatments for cancer and infectious disease. And it’s not just the chemistry that is complex. The Olson Lab experiments with nature-inspired bioengineered mini-proteins modified with synthetic chemistry to produce “Optides” (optimized peptides), which hold promise for optimizing therapeutic properties. Managing all the experimental data and metadata presents a myriad of challenges which LabKey Server is well suited to handle.

Customized LIMS Software for Protein Engineering

The Olson Lab has developed Optide-Hunter, a LIMS software built with LabKey Server. The platform supports a generalized protein compounds workflow for tracking entities and assays from creation to preclinical experiments.

You’ll find a compound registry, in-silico and in-vivo assays, support for high-throughput and large-scale production, and automated data loading. Optide-Hunter also supports automated chromatogram classification and external pre-processing of high performance liquid chromatography (HPLC) data. Other users can customize the software for their unique workflows.

You can learn more about the project and partnership with LabKey in the case study. Continue reading to learn how to explore the Optide-Hunter yourself right now.

Getting Started

You can explore a read-only version of the Optide-Hunter yourself right now with no account or registration required.

  1. Click here to open the Optide-Hunter in a new tab. Keep these instructions alongside.
  2. Click the Optides project icon at the bottom of the screen. The home page shows the project files, including custom R code and custom module examples you can download.
  3. Each topic along the top menu bar covers a different aspect of the project. Hover over CompoundsRegistry and click Samples to see the registry of compounds for protein expression and conjugation. A set of wiki pages listed on the right guide you with details about the elements shown.
  4. For example, lineage relationships are represented by ordering compounds in a specific hierarchy. Before variant sequences are registered, corresponding homologues must be registered and assigned IDs.
  5. Next, explore the assays along the menu bar. For example, HTProduction > Assays. Click HPLC Assays on the Assay List, then view and filter the data to find compounds of interest.
  6. On the Programs menu, select the QueryAssays option then enter one or more Compound IDs, for example “CNT0001356” and click Submit. Two grids of Matching Constructs and InsilicoAssays Matches will be populated with the search results to give you a common view.

Create Your Own Trial of Optide-Hunter

After exploring our read-only example, you can create your own trial instance and try uploading your own data, customizing the user interface, and developing your own queries and reports. To launch your 30 day trial, create or log in to your account via this link, then select the “Optide-Hunter – Case Study” option.

This project was published in the journal BMC Bioinformatics with the title “Laboratory Information Management Software for Engineered Mini-protein Therapeutic Workflow“. Learn more about the collaboration with LabKey in our case study.

LabKey European User Conference Events

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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.

American Society for Mass Spectrometry Conference 2019

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From June 2-6, 2019, LabKey Vice President Josh Eckels will be in Atlanta for the Annual Conference of the American Society of Mass Spectrometry. He will attend the the Skyline User Group Meeting and present a poster highlighting new quality control features for targeted mass spectrometry.

Meeting: Skyline User Group

Sunday, June 2
Georgia Aquarium, Atlanta

Panorama is a web-based complement to Skyline, used by more than a hundred organizations to manage, analyze, and share targeted mass spec data generated by Skyline. Since being unveiled at ASMS 2015, Panorama’s support for QC workflows has expanded significantly.

Read more in the Skyline User Group Meeting Summary >

Poster: Customizable quality control metrics and notifications with Panorama, AutoQC, and Skyline

Monday, June 3
Poster Number: 430

Introduction: Panorama’s newest quality control (QC) capabilities further extend its automated system suitability monitoring for targeted mass spectrometry assays. Panorama first added its QC folder type in 2015 in conjunction with AutoQC, a utility that monitors for newly-acquired system suitability runs targeting operator defined sets of peptide and small molecule standards. New runs are automatically analyzed using Skyline and imported into Panorama. Recent work greatly expands the metrics that can be monitored. Coupled with new types of statistical analyses and email alerts of outliers in newly acquired data, Panorama now offers an even more robust workflow. 

Methods: Panorama now supports metrics that track values associated with the entire run such as statistics related to iRT regression, single replicate calibration and pressure traces, adding to its existing support for metrics associated with individual peptides and small molecules. Users can visualize their data using statistical process control plots, customize the metrics applied, subscribe to email notifications, and export in a variety of formats.

Conclusions: Panorama offers a growing collection of customizable QC metrics and has expanded beyond values associated with individual peptides and small molecules. Users can assess quality for data that is specific to their experimental design, opt-in and opt-out of the full library of metrics to eliminate false positives and focus their system suitability checks on the most diagnostic data. Panorama helps users consolidate their workflows to reduce the data processing bottlenecks that occur in many laboratories.

As of June 2019, more than 350 labs are using Panorama projects to manage targeted mass spectrometry assays and major pharmaceutical companies and other organizations have deployed their own in-house installations of Panorama.

Read more and see the full poster >

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.

Learn more about joining the Panorama Partners >

Overcoming Key Challenges in Mass Spectrometry Data Management

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[vc_row css=”.vc_custom_1559248243125{padding-top: 20px !important;}”]Targeted mass spectrometry methods provide reproducible and quantitative analyses for a wide range of proteins and small molecules of interest. Mass spectrometrists need tools to help manage the data they generate, analyze it, and leverage their findings when designing new assays.

There are many approaches to mass spec, including Selected Reaction Monitoring (SRM), Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), and Data Independent Acquisition (DIA/SWATH), each of which generates varying amounts of data for analysis. The variability, scale, and reproducibility requirements of these methods require a data management solution that is flexible, robust, and secure.

LabKey Server’s solution, Panorama, integrates closely with Skyline, a leading analysis application developed by the MacCoss lab at the University of Washington. With Panorama, LabKey supports the data management needs of mass spectrometrists by:

Centralizing Storage and Querying

LabKey Server acts as a shared data repository for Skyline documents, providing:

  • A shared workspace for teams to collaborate on their analyses
  • Tracking of multiple document versions of the same analysis
  • Easy methods for sorting, filtering, querying, and accessing results via APIs
  • Retrieval of previously analyzed data for reuse in Skyline

Tracking System Suitability

LabKey Server tracks system suitability with Panorama using:

  • Longitudinal tracking of key metrics including retention time, peak area, and mass accuracy
  • Automated import and analysis of newly acquired samples via integration with AutoQC Loader and Skyline
  • Visualizations and statistical process controls like Levey-Jennings, CUSUM (cumulative sum), and moving range plots

Supporting Published Manuscripts

Using LabKey Server, Panorama Public meets the requirements for data submission with:

  • Workflows for securing data prior to publication, then sharing it after review
  • Compliance with ProteomeXchange requirements for submissions, including raw files
  • Stable storage for supplemental data to accompany published manuscripts

LabKey Server helps research teams efficiently manage, analyze, and publish targeted mass spectrometry data at scale, maximizing its value. To learn more about using LabKey Server to manage targeted mass spectrometry data, check out the documentation library on the LabKey Support Portal or request a demo.[vc_column width=”1/6″][vc_column width=”4/6″][vc_cta h2=”Find Us at ASMS 2019″ add_button=”bottom” btn_title=”Contact Us” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_align=”center” btn_link=”url:%2Fabout%2Fcontact%2F|||”]LabKey’s lead for Panorama, Josh Eckels, will be in Atlanta for the Annual Conference of the American Society for Mass Spectrometry. You can find him:

  • At the Skyline User Group meeting on Sunday, June 2
  • At his Monday, June 3 poster 430 (Customizable quality control metrics and notifications with Panorama, AutoQC, and Skyline)
  • By setting up a separate time to meet by contacting LabKey

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Barriers to R&D Productivity: Inefficient Data Handoffs

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The drive to discovery of new biologic therapeutics involves massive amounts of data passing step by step through a lengthy and sometimes iterative process involving large or distributed teams. Economies of scale and team member specialization can reduce the overhead of research and development, but only when every transfer of data is clear and efficient, with reliable audit logging to track the process.

Modern data collection techniques and processes can overwhelm data management solutions and handoff procedures that weren’t designed for the volume of modern high-throughput research.

  • How do you know you have all the necessary data for an experiment or analysis task?
  • How can you tell if you have the right version of data?
  • What other tasks have been completed on this data, and was anything learned in a related experiment that I should know about?

Traditional methods for transferring data, such as email or direct meetings with collaborators, may not suffice when questions arise later. Recording exactly what happened and capturing all ad hoc sharing of information will prevent other team members wasting time tracking down answers.

LabKey Biologics is specifically designed to make data handoffs seamless and consistent. Sharing a central data repository and using common and fully audited workflow procedures means everyone involved, including new team members, can easily find required data and learn everything they need to know about it.

Centralized access to data makes collaboration seamless

LabKey Biologics makes data handoffs efficient in R&D laboratoriesUsing a data sharing hub, team members never need to wonder where to find the data they need. Clear and consistent gathering of experiment metadata means that not only do they see what they need, they immediately know when it’s ready for the next task or experiment. With LabKey Biologics, team members share access to the entity designs, biological samples, and analytical results they need for further research.

Tasks assignments are clear in a workflow request system

Ensuring that everyone knows who is doing which tasks and in what order is critical to efficient research. Team members using Biologics can rely on the workflow request system to clearly track responsibilities – avoiding both duplication of effort and the risk of missing key steps.

Self-service access to past work of others

When teams are large and distributed, even knowing who to ask about past work can be complex. By keeping all details about every experiment with the data itself, teams using LabKey Biologics ensure that everyone has the information they need at their fingertips.

With LabKey Biologics, R&D teams reduce the time spent on repetitive data management tasks and devote more time to discovery. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.[vc_column width=”1/6″][vc_column width=”2/3″][vc_cta h2=”Upcoming Webinar” add_button=”bottom” btn_title=”Register for a Session” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_align=”center” btn_link=”url:https%3A%2F%2Fzoom.us%2Fwebinar%2Fregister%2FWN_EKhv0KeiSQaOrav-oOEmCg||target:%20_blank|”]Join LabKey Product Manager, Ryan Luce, Ph.D, for an introduction to LabKey Biologics! Explore the entity registration, data integration, and workflow management capabilities of the LabKey Biologics system.[/vc_cta][vc_column width=”1/6″]

What’s New in LabKey Biologics 19.1

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LabKey has continued to improve and enhance the LabKey Biologics application with the release of version 19.1! We continue to work with our users to prioritize the most needed features and solutions for R&D teams.

Highlights

  • Users can now create a custom chart or a view of a data grid once, and then see that view anywhere that’s relevant within Biologics. This allows you to design a report or graph, but be able to repeatedly see that analysis filtered to the samples in any particular experiment.
  • Media and batch creation enhancements better match real world needs for flexibility with clarity. Import ingredient and raw material information in bulk, include “unknowns” for mixtures when necessary, and enter additional ingredients to a recipe during creation of a batch.
  • Sample set operations have also been improved, with easier-to-read views of associated assay data as well as improved performance for importing and updating samples.
  • Scientists need the flexibility to store arbitrary file types with their work, including published articles, SOPs, supplemental datasets, and images. You can now attach any number of files to a specific experiment, providing context and analysis of what occurred.

View Full Release Notes >

Upcoming Events

Webinar: Intro to LabKey Biologics: May 2, 2019

LabKey Biologics WebinarJoin LabKey Product Manager, Ryan Luce, Ph.D, for an introduction to LabKey Biologics! Explore the entity registration, data integration, and workflow management capabilities of the LabKey Biologics system.
Learn More & Register

LabKey User Conference, BaselLabKey User Conference & Training – Basel

June 4-5, 2019 | 2 Days
Basel, Switzerland
Learn More & Register!

LabKey User Meeting, LondonLabKey User Meeting – London

June 6, 2019 | FREE
London, UK
Learn More & Register!

LabKey User Conference and Workshop, SeattleLabkey User Conference & Workshop – Seattle

October 3-4, 2019 | 2 Days
Seattle, Washington, USA
Learn More & Register!

More on the Blog

Barriers to R&D Productivity: Manual Data Integration Strategies

Barriers to R&D Productivity: Lack of Visibility into Previously Generated Data

Barriers to R&D Productivity: Lacking a Central Point of Access to Data

Barriers to R&D Productivity: What’s Slowing Down My Research?