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Overcoming Key Challenges in Mass Spectrometry Data Management

Posted on May 30, 2019June 10, 2024 by admin

[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

Posted on May 28, 2019June 10, 2024 by admin

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

Using 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

Posted on April 25, 2019June 10, 2024 by admin

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

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.
Learn More & Register

LabKey User Conference & Training – Basel

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

LabKey User Meeting – London

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

Labkey 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?

Barriers to R&D Productivity: Manual Data Integration Strategies

Posted on April 16, 2019June 10, 2024 by admin

There is no single test that is run to assess the safety, stability, and scalability of a biologic treatment. Instead, these key characteristics are measured using a variety of analytical and observational tests. In order to assess the biologic’s viability as a therapeutic, scientists must be able to analyze all of these data points in conjunction with one another. When R&D teams are utilizing spreadsheet based systems for data management, this aggregate analysis requires manual integration of data from multiple datasets stored in a variety of formats.

Manually integrating datasets can pose a number of productivity challenges for R&D teams.

Manual integration is often a time-consuming process that can take valuable time away from your scientists.
It is difficult to ensure that data is integrated in a consistent manner across projects and team members.
Manual manipulation of data means a higher chance of human error.

LabKey Biologics automates the integration of datasets, and prepares data for analysis in an efficient and reliable manner. Automating the integration of data with LabKey Biologics can enhance R&D productivity in the following ways.

Saving Your Scientists Time

LabKey Biologics stores R&D data including molecular entity definitions, sample details, and analytical results in a consistently structured manner, preparing it for seamless integration with related data of other types. The system then automatically builds relationships between related data, so that scientists can easily explore data through the UI or export integrated data for analysis using external tools. Automatically building connection between structured data types saves scientists hours of time that would be spent on manually integrating data, and allows them to dedicate more time to analysis.

Ensuring Consistent Data Processing

Relationships between data types stored in LabKey Biologics are defined on a global level, ensuring that data connections are built consistently across all projects. Users can also design custom grid views of data to surface data points of interest in a single grid. These custom views can be saved and applied across groups of samples or experiments, ensuring that data is presented consistent across a research project.

Minimizing Human Error

Perhaps the most straight-forward benefit of utilizing LabKey Biologics for research data integration is minimizing the potential for human error. Manual integration can lead to copy/paste mistakes, problemattic auto-formatting, and other errors that can be hard to detect and significantly hinder analysis. Using LabKey Biologics to integrate datasets eliminates the risk of these types of errors during the integration process, and provides additional mechanisms to protect against human error during data analysis including audit logging of data access and transformations.

With LabKey Biologics, biopharma R&D teams can automate data integration, accelerating the integration process and ensuring the generation of high quality datasets. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.

Overcoming Key Challenges in NAb Data Management

Posted on April 11, 2019June 10, 2024 by admin

Biopharmaceuticals are increasingly being prescribed for a variety of diseases, from autoimmune disorders such as arthritis to neurological conditions like Alzheimer’s. Neutralizing antibody (NAb) assays are a critical component of biopharmaceutical development, helping inform researchers of potential product efficacy and patient safety. Having reproducible, repeatable NAb assay results will improve the product research pipeline and ultimately impact trial and patient outcomes. For this reason, efficient NAb data management is more important than ever to biomedical researchers.

With the advancement of plate and instrument technologies, NAb assays provide a high-throughput mechanism of evaluating the potential immunogenicity of the drugs they study. Teams must be able to set up plates accurately, produce consistent analyses, ensure appropriate quality controls, and keep track of data provenance in order to deliver NAb assay results that are reproducible, comparable, and reliable.¹ LabKey Server helps teams overcome core challenges in generating reliable NAb data in the following ways.

Facilitating Good Record Keeping Practices

LabKey Server helps scientists maintain good record keeping by:

Directly importing instrument-derived results files and collating them into an analysis dashboard
Improving data integrity by associating raw data files and results
Providing a built-in graphical template designer that allows users to quickly create new plate layouts (supporting options for cross- or single-plate dilutions, and single- or multiple virus plates)

Streamlining NAb Data Analysis & QC

Improve the consistency and ease of NAb data management and analysis using LabKey Server by:

Automatically calculating and generating neutralization curves and titers
Removing ill-fitted and otherwise unsuitable data and maintaining those changes for future quality assurance
Translating complex plate maps with dilutions and/or multiple viruses into the NAb dashboard so that results of each run may be viewed and graphed on a per-virus basis

Enabling Collaborative Analysis

LabKey Server can help researchers collaborate and share NAb data by:

Centralizing raw file storage and analysis in a secure web-based interface
Providing an interactive NAb Dashboard for collaborators to interrogate the data
Integrating NAb data with other data types, presenting users with a comprehensive view

High-throughput 384-well NAb assays may contain hundreds of samples with dilutions across plates or within a single plate and the resulting graphs and views can be complex. The LabKey NAb Assay tools provide quick visual feedback allowing you to confirm a valid run or immediately correct and rerun if necessary. To learn more about using LabKey Server to manage NAb data, check out the NAb documentation library on the LabKey Support Portal or request a demo.

¹https://bmcimmunol.biomedcentral.com/articles/10.1186/1471-2172-12-33

Project Highlight: Harvard Pilgrim Health Care Institute and FDA MyStudies Mobile App

Posted on March 28, 2019June 10, 2024 by admin

Project Background

In 2017, Harvard Pilgrim Health Care Institute (HPHCI) was selected by the U.S. Food and Drug Administration (FDA) through the FDA-Catalyst program to lead the development of a mobile application, called FDA MyStudies, that would facilitate the collection of real-world data directly from patients to support clinical trials, observational studies, and registries. The effort was funded by an award to FDA scientific staff from the Patient Centered Outcomes Research Trust Fund which is administered by the Associate Secretary for Planning and Evaluation (ASPE) of the Department of Health and Human Services. Harvard Pilgrim selected the mobile application development firm Boston Technology Corporation (BTC) and LabKey as their development partners for the project. BTC was tasked with developing a user friendly mobile interface while LabKey was tasked with building a secure back-end storage environment for collected data.

Why LabKey

LabKey Server was selected as the back-end data management solution for this project for a number of key reasons, one of which being the platform’s flexible, science-specific architecture. With the project’s long-term goal of expanding the use of real-world data across research programs, the application framework needed to support a broad range of potential healthcare topics through configuration as opposed to requiring development for each new project.

LabKey Server also stood out as an ideal solution because of the platform’s ability to handle PHI/PII data in a manner compliant with HIPAA and FISMA regulations. Finally, one of the project requirements outlined by the FDA was that the resulting application and storage architecture would need to be made available as open source to the scientific community. LabKey Server, an open source platform licensed under Apache 2.0, was able to support this distribution model without any changes to the existing licensing model.

The Implementation

The back-end storage environment is composed of three independent web applications:

Response Server: used to store data captured via the mobile application and provide secure access to these data for data analysis purposes.
Registration Server: used to manage participant authentication, preferences, notifications, and consents.
Web Configuration Portal: used to design study questionnaires and store study configuration information including consent forms, eligibility tests, surveys, and study resources.

This dispersed data model ensures secure partitioning of all identifying information from response data, helping ensure patient privacy. LabKey Server provides role-based governance of the data stored on the Registration and Response servers and ensures that data are only accessible by authorized users. When it comes time for analysis, data stored in the response server can be accessed by authorized users via a number of different methods including LabKey’s built in analytics capabilities, download to SAS or R, or export to Excel or other standard format.

The bulk of the components used in the development of the secure data storage environment were previously existing in the LabKey Server platform. However, three key areas of custom development and extension were required to support the project’s use:

Enrollment Tokens: A unique token that is assigned to each participant upon registration that can be used to restrict their enrollment to a specific study cohort, as well as match the collected study data to external systems (e.g., EHRs).
Automatic Schema Creation: Automatic generation of a new database schema when a study questionnaire is created, eliminating the need for manual schema development.
Mobile App Response Handling: Capabilities to support automated parsing of the JSON responses sent by the mobile application were implemented, enabling the storage of results in the schema, in a scalable manner.

The LabKey team delivered these developments in a custom module using an agile development methodology, refining them based on client feedback in tandem with the development of the mobile application UI.

Results

To evaluate the usability and viability of the application and data storage environments, Harvard Pilgrim contracted with Kaiser Permanente Washington Health Research Network (KPWHRN) to launch a pilot study examining the medication use and healthcare outcomes of pregnant women throughout their pregnancy. For the pilot program, the Harvard Pilgrim team utilized LabKey’s Compliant Cloud hosting services to manage the storage of study data in a secure AWS cloud environment. Participants who successfully completed the study reported high levels of usability and comfort sharing sensitive information using the app. The pilot was deemed a success, and in Fall 2018 the FDA released the open source code and documentation publicly for use in other studies. Since its release, the FDA MyStudies platform has been selected to support a clinical trial as well as a disease registry.

Webinar Presentation

On May 9, 2019, subject matter experts from the FDA, HPHCI, BTC, and LabKey, presented an overview and many details about this project in a live webinar entitled: An Introduction to the FDA MyStudies App: An Open-Source, Digital Platform to Gather Real World Data for Clinical Trials and Research Studies.

Learn More Here!

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

Posted on March 5, 2019February 22, 2024 by admin

Developing a safe and effective biotherapeutic involves the collection of data from many different team members and research functions. At larger biopharma organizations, there are often multiple team members working on similar tasks in a functional area.

In order for collaborative R&D to operate efficiently, team members need visibility into what data has been generated across the research group. LabKey Biologics provides a central hub for storing R&D data with an easy to navigate structure and dynamic querying capabilities to help team members locate data of interest. Providing greater visibility with LabKey Biologics can enhance R&D productivity by:

Preventing Duplicate Work in the Lab

There are several ways in which the visibility into previously generated data provided by LabKey Biologics can prevent duplicate work in the lab. Perhaps a bench scientist is interested in understanding what protein expression occurs under a particular set of conditions. Unbeknownst to them, an experiment testing that same protein expression was completed 6 months earlier by another team member. Using LabKey Biologics, this researcher could search historical experiments with those same conditions and view their results, saving them the time and resources of conducting a new experiment.

LabKey Biologics can also prevent teams from running duplicate experiments on the same sample. Each sample in LabKey Biologics stores a complete record of all of the assays that have been run against them. Technicians can use this information to verify that an assay has not already been run.

Protecting Against Dirty Data

A lack of visibility into your team’s previously generated data can also lead to duplicate records in your bioregistry. LabKey Biologics provides easy mechanism for searching/sorting existing data to locate previously registered entities, and also conducts an automated uniqueness check on each entity registered in the system. These tools ensure that related data is connected to the correct entity from the start, and removes the need for downstream data clean-up.

With LabKey Biologics, biopharma R&D teams can reduce redundant experimentation saving valuable time and resources. Request a demo of LabKey Biologics or explore the LabKey Biologics trial environment, free for 30-days.

Overcoming Key Challenges in Luminex Data Management

Posted on February 18, 2019November 27, 2024 by admin

With massive increases in data collection, scientists must diligently apply Luminex data management practices, well-defined quality controls, and consistent analyses¹ in order to be efficient and effective. The Luminex xMAP technology is widely used in research, clinical trials, and diagnostics as it provides a multiplexed immunoassay platform to measure complex humoral responses. With instrumentation and bead technology improving, scientists are able to measure larger numbers of analytes on a greater number of samples.

Although typical Luminex xMAP exports are easy to read, they are often exported as multi-tab files that require human interaction and manipulation of the data in order to perform comprehensive analysis. Standard analysis mechanisms that involve manual processing of data are arduous and prone to errors. Results and visualizations of Luminex data are often shared without comprehensive annotations on how the analysis was performed; leaving out valuable background information such as well-exclusions, curve fits, and background calculations. Utilizing LabKey Server for Luminex data management helps standardize the workflow of transforming instrument-generated outputs into valuable data visualizations and ensures that valuable contextual information is preserved.

Enhancing Luminex Data Management

The LabKey Server software platform helps research teams enhance their management of Luminex data by:

Providing support for multi-tabular excel output files and converting them into easy-to-read grids
Allowing users to attach metadata about Luminex runs, increasing traceability of data
Providing a single platform where raw data, transformed data, and analyzed data are linked and easy to track

Improving Quality Control of Luminex Data

LabKey Server’s Luminex data management tools help labs improve quality control of their data by:

Automatically flagging outliers based on expected values
Tracking data exclusions made by users
Providing users with tools to track QC metrics across runs using Levey-Jennings plots

Ensuring Provenance & Reproducibility of Luminex Analyses

LabKey Server helps teams maintain data provenance and conduct reproducible analysis by:

Logging changes to data records and allowing scientists to view the history of data transformations from the raw file to the analyzed results
Providing built-in visualization tools that can be reused across runs
Providing mechanisms to securely share data with colleagues, collaborators, or manuscript-reviewers

With the right tools, scientists can maintain a comprehensive, error-free catalog of Luminex data and analyses. To learn more about using LabKey Server to manage Luminex data, check out the Luminex documentation library on the LabKey Support Portal or request a demo.

¹ Eckels J, Nathe C, Nelson EK, et al. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics. 2013;14:145. Published 2013 Apr 30. doi:10.1186/1471-2105-14-145

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

Posted on February 7, 2019June 10, 2024 by admin

Developing a biologic therapeutic requires the coordinated efforts of many team members. From concept to confirmation, each stage involves the generation, analysis, and dissemination of large quantities of data between the members of your research and development team.

Creating a central point of access for data generated across team members streamlines data sharing and significantly improves your team’s productivity. LabKey Biologics serves as a “single source of truth” for R&D data, from details about molecular entities to the samples that have been generated and the experiments that have been run. One of the productivity benefits of implementing LabKey Biologics is the clarity it provides to team members about where to store data and where to find data.

Team Members Know Where to Store Their Data

Without a data sharing hub, team members often find themselves relying on several different distribution methods to disseminate data to different groups, adding steps to the data sharing process and slowing productivity. Providing a central system for data storage that is accessible by all team members provides data generators with a consistent, repeatable process for distributing data. With LabKey Biologics, team members can centrally manage all of the data they generate about entity designs, biological samples, and analytical results, as well as group data by experiment and add relevant metadata to enhance discoverability.

Team Members Know Where to Find Data

A central point of access for research data eliminates the wasted time searching for data in a variety of different storage locations (emails, local drives, cloud-based file shares…). Team members using LabKey Biologics can rely on the consistent data structures established by the system to locate data of interest and omni-bar searching to easily locate row level data within datasets.

With LabKey Biologics, teams can reduce the time spent on tedious 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.

LabKey Vulnerability Management & Recent Issue Resolution

Posted on February 6, 2019June 10, 2024 by admin

Our Commitment to Cyber Security

The security of our users’ data is of utmost importance to us at LabKey. LabKey Server has functioned as a secure platform for research teams for 15+ years and the LabKey team works diligently to to adapt the platform in order overcome the evolving security challenges of a web-based world.

LabKey releases three major versions of the LabKey Server platform each year, each of which is subjected to extensive automated and manual testing to identify potential bugs and platform vulnerabilities for correction prior to each release. On rare occasion the LabKey team may identify or be notified of an issue that poses a risk to our users’ security. When this occurs, the LabKey team will assess the issue and determine a timeline for resolution based on the severity of the risk. Issues that pose a high security risk to our clients are corrected and delivered via a patched version of the current release to clients and community users as soon as possible.

Recent Security Vulnerabilities and Resolution

As a community driven platform, we welcome the collaboration of groups like Tenable, who recently brought to our attention several security vulnerabilities with the LabKey Server 18.2 release. These security issues were resolved in accordance with LabKey’s standard operating procedure for security vulnerabilities; the most serious was addressed with an immediate hotfix to the 18.2 release and the remaining issues patched in LabKey Server 18.3.0-61806.76, released January 16th.

The three vulnerabilities that were recently disclosed stemmed from different causes, with varying levels of risk. The most serious was a cross-site scripting (XSS) vulnerability that could have allowed a malicious entity to create a URL that, if accessed by a LabKey Server user (via a link in an unsolicited email, for example), would cause their browser to execute JavaScript of the attacker’s choice. This issue was hotfixed in version 18.2.

The second issue allowed a malicious entity to create a URL that would initially send a user to a LabKey Server installation, but then redirect them to a third-party server, such as one controlled by the attacker. Users might have inspected the link sufficiently to see that it went to a trusted LabKey Server deployment, but not realized that their browser would later be sent elsewhere.

The third issue was a bug that did not fully handle all possible inputs from a site administrator setting up a network drive mapping on LabKey Server installations on Windows. It would have allowed them to run command-line programs on the server. LabKey assessed this issue as a very low risk, since site administrators are implicitly trusted on all installations with the highest level of access possible within LabKey Server. While the likelihood of this bug resulting in a malicious attack was very low, the LabKey team chose to correct the issue in order to eliminate the risk.

While these specific issues are no longer a threat to the security of our users, we continue to evaluate the security of the platform and address risks as new malicious threats arise. We encourage users to always update to the latest version of LabKey Server to ensure that they have the most up-to-date protection against cyber security threats.