Tag: Server SDMS

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:

1. Response Server: used to store data captured via the mobile application and provide secure access to these data for data analysis purposes.
2. Registration Server: used to manage participant authentication, preferences, notifications, and consents.
3. 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!

Related Reading

https://www.fda.gov/downloads/Drugs/ScienceResearch/UCM625206.pdf

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.

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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

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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

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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

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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

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.

Flow cytometry data is widely used across diverse set of research areas including drug discovery and personalized medicine. Ongoing improvements to instrument technology allow scientists to generate more and more targeted reagents which in turn leads to increasing amounts of high-dimensional flow cytometry data. As the application of flow cytometry in immune monitoring becomes more prevalent, many scientists are finding themselves asking “what is the best way to manage flow cytometry data?”

As teams evaluate software tools for managing flow cytometry data, there are several things to keep in mind. Instrument-generated fcs files from cytometers are generally not useful to scientists on their own. Typically, users interrogate their data by creating an analysis file, either with manual gating through commercially-available tools like FlowJo and FCS Express, or by performing computational analyses via free software packages like Bioconductor. Ensuring that data provenance is maintained between fcs files and analysis is vital, and provides valuable information for groups looking to validate or re-analyze the raw data in the future.

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Maintaining Comprehensive Data Records

The LabKey Server software platform help groups ensure data provenance and maintain comprehensive flow cytometry records by:

• Allowing for import of raw fcs files as well as analysis files
• Validating all fcs files are present when linking data to a FlowJo workspace file
• Auditing file upload for analysis data used in a LabKey study
• Surfacing run parameters and compensation values for further quality control

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Adding Value to Runs

LabKey Server’s flow cytometry tools can also helps add value to runs by:

• Providing mechanisms to insert keywords and adding metadata
• Ensuring gate naming is consistent across workspaces
• Allowing administrators to merge gating strategies when necessary
• Visualizing statistics in Levy-Jennings plots for valuable quality control metrics

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Improving Data Analysis Workflows

Using LabKey Server, scientists can achieve further improvements to their analysis workflow by:

• Integrating flow cytometry statistics and 2D plotting within the LabKey Server platform
• Creating easy integration mechanisms across flow cytometry runs, panels, and projects
• Providing built-in visualization tools for users to interrogate their data

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With the right tools, scientists can maximize the insight derived from their flow cytometry data. To learn more about using LabKey Server to manage flow cytometry analysis, check out the flow cytometry documentation library or request a demo.

LabKey Server is a Java-based web application. Recent changes to Oracle’s Java licensing model and release schedule require changes by software providers like LabKey, as well as application administrators. Below LabKey’s VP of Product Strategy, Adam Rauch, explains the recent changes, how LabKey plans to address them, and what actions need to be taken by teams running LabKey Server to ensure on-going stability and support.

Recent Changes to Java Release Cadence and Licensing

Last year, Oracle announced several significant changes to the Java release and support model that introduce complexity to the previously straightforward process of deploying a Java runtime. Organizations will need to make decisions and revise their upgrade processes, but we believe these changes will lead to a stronger Java platform, one that will be more responsive and easier to support in the long term.

Perhaps the biggest news is that Oracle now requires a paid subscription for all use of the Oracle Java Runtime (“Oracle Java SE”) in production environments. Starting with Java 11 (released September 2018), organizations are required to pay up to $25 per CPU per month for production server or cloud use of Oracle Java SE. This seems to apply to everyone… no exceptions for academic, non-profit, or small organizations. With a subscription, Oracle will provide long-term support (LTS) for designated versions of their runtime (Java SE 8, 11, 17).

With Java 9, the release cadence transitioned from major versions every five or six years to more incremental feature releases every six months. According to Oracle, this new time-driven release model allows more rapid innovation, but it also means organizations will need to upgrade more quickly to keep pace with the changing platform.

This diagram (brought to you by the LabKey Visualization API) helps illustrate this change, with each bar capturing the time Oracle publicly supported (or plans to support) each version:

Note that in addition to more rapid and shorter releases, Oracle has eliminated the overlap between versions. Under the new model, public support for previous releases ends immediately upon release of a new version. As a result, Java 9 was end-of-lifed (no further support) the day Java 10 was released and Java 10 was end-of-lifed the day Java 11 was released.

Other Options and LabKey’s Response

As a Java-based web application, every deployment of LabKey Server is affected by these changes. You can certainly move to a paid subscription with Oracle, but many of you have told us you want a free Java option. LabKey has heard you and, starting with LabKey Server release 18.3, you now have the ability to deploy with a completely free, open-source Java runtime.

This is possible because Oracle has embraced OpenJDK, the open source implementation of the Java platform. Oracle recently contributed its remaining commercial features to the OpenJDK project and now builds its subscription Oracle Java SE from the OpenJDK sources. In fact, Oracle distributes two versions of OpenJDK: the Oracle Java SE requiring the commercial license and a production-ready open-source build of OpenJDK licensed under GPLv2 with the “Classpath Exception” (“Oracle OpenJDK”). The code is the same; the Oracle OpenJDK distribution merely lacks the long-term support provided under the subscription. Oracle might add proprietary enhancements (e.g., advanced garbage collection algorithms, just-in-time compilation, profilers, and other tools) to future commercial runtimes, but at the moment, these distributions should be interchangeable.

In response to these changes and our clients’ requests, LabKey has shifted our development, testing, and hosting to focus on Oracle OpenJDK 11. We will continue limited testing on the commercial Oracle Java SE releases, but the vast majority of our attention will be focused on OpenJDK. We plan to support future OpenJDK releases at or shortly after they’re released. Where possible, we’ll hotfix the current production release of LabKey Server to ensure it’s compatible with newly released versions of OpenJDK. (For example, even though it won’t be released until March 2019, we’re already testing OpenJDK 12 early-access builds against our 18.3 and pre-19.1 builds.)

Since older OpenJDK releases will not receive public support from Oracle (i.e., no security patches), LabKey will stop supporting them shortly after they’re end-of-lifed. To ensure you have all the latest Java security patches and bug fixes, you must regularly upgrade to the latest Java runtime release. You’ll need to upgrade to each six-month feature release plus the intervening security releases (two or three per feature release… roughly every two months).

Based on the published Java release schedule, Java support in LabKey Server for the next year will likely roll-out as follows (where “Java X” means “OpenJDK X and Oracle Java SE X”):

LabKey Release	Java Versions Supported	Changes
18.3 – Nov 2018	Java 11, Oracle Java SE 8	Add Java 11
19.1 – Mar 2019	Java 11 & 12	Add Java 12, Remove Java 8
19.2 – Jul 2019	Java 12	Remove Java 11
19.3 – Nov 2019	Java 12 & 13	Add Java 13

You can always visit our Supported Technologies page to review the latest plan.

Since OpenJDK is a true open-source project, many organizations other than Oracle are now building, distributing, and supporting it. A few of the most prominent examples:

• AdoptOpenJDK has promised community-driven LTS builds of OpenJDK
• Red Hat and other Linux distributions provide and support OpenJDK
• Azul Zulu, IBM, SAP, et al offer free and commercial options
• Amazon recently announced Corretto, a no-cost distribution of OpenJDK that includes long-term support

All of these implementations derive from the same OpenJDK source, so, in theory, they should be interchangeable. However, it’s important to understand that LabKey has not yet tested any of the non-Oracle distributions and, therefore, we do not support them. We plan to test more of these distributions over the next year. But for now, you will need to utilize one of the two Oracle distributions.

Recommendations for Your Team

It’s time to take action on these changes. Java 11 is here and Java 12 is coming soon. Java 8 will reach “End of Public Updates” for commercial users in January 2019, and will stop being a viable option for most deployments. Our recommendations:

• Discuss Java licensing with your legal, licensing, and IT teams. They may have already put in place a runtime subscription or developed a policy around Java. If not, they need to understand these changes and create a plan.
• Based on your organization’s policies, choose the runtime that’s appropriate for your deployments going forward: Oracle OpenJDK 11 or Oracle Java SE 11.
• Upgrade to LabKey 18.3 and then switch to that Java 11 runtime.
• Keep upgrading your runtime… every two months to stay secure.
• If you’re building Java modules, switch your development and testing to JDK 11. IntelliJ makes it easy to configure multiple JDKs and switch between them, if you still need to build with JDK 8 for other work.

Comments? Suggestions? Questions? Please share them on the LabKey support forum . 

Emerging infectious diseases rapidly rise to prevalence and spread quickly across a population. In order to minimize their impact on public health, scientists must reach across geographical and organizational boundaries to share data that will help the global research community understand, contain, and ultimately cure aggressive infectious diseases. This type of large scale collaboration requires a robust research platform to centralize data and facilitate the shared generation of insight.

LabKey is helping teams around the globe combat emerging infectious diseases by providing a web-based data management platform to help overcome key collaboration challenges, including:

Integrating Heterogeneous Data

Scientists, public health officials, and medical professionals must be able to collect and integrate data from multiple sources (clinics, labs, etc.) in order to develop a comprehensive understanding of an emerging infectious disease. By housing data in one centralized location, researchers and collaborators can improve pathogen tracking and disease surveillance.

LabKey Server facilitates the collection and integration of data from a variety of sources by providing:

• Specialized import tools to integrate data from a variety of immunoassay types, including ELISA/ELISpot, luminex and flow cytometry
• Demographic datasets to capture metadata about individuals within a population
• A study framework that connects demographic, clinical, and analytical data in order to monitor the disease and/or treatment status of individuals over time

Creating an Adaptable Database

During the early stages of a disease outbreak data is collected rapidly and abundantly. As the scientific community’s understanding of a disease increases, the data collection needs of researchers will shift as they determine which pieces of information are most valuable. The central data management system used by infectious disease researchers must provide both high levels of flexibility and structure in order to keep up with these broad and evolving data needs.

LabKey Server provides a highly flexible environment for data capture, allowing teams to evolve their research environment using:

• A configurable and customizable user interface
• Powerful query tools to merge and present data
• APIs to import data from a wide variety of external sources and formats

Real-Time Data Sharing

In recent years, researchers working in the field of emerging infectious disease have begun to forgo traditional data publishing processes during times of a public health crisis, in favor of real-time data sharing. Real-time sharing of research observations and analytical data is helping accelerate the pace of understanding and development of treatments for aggressive infectious diseases.

LabKey Server facilitates real-time data sharing by providing:

• Study publication tools that allow research teams to curate and publish public-facing datasets without compromising the security of their original data
• Dynamic or static reports and visualizations to quickly summarize data for collaborators
• Easy export of data to common research formats for ancillary investigation

[vc_cta h2=”Explore LabKey Server” add_button=”bottom” btn_title=”Start Your Trial” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_shape=”round” btn_align=”left” btn_link=”url:https%3A%2F%2Fwww.labkey.com%2Ftrial-sign-up%2F|||”]With the right tools, research teams have the ability to more rapidly understand and eradicate emerging infectious disease. Sign-up for a free trial to see how LabKey Server can help your team overcome these and other key research challenges.[/vc_cta][vc_custom_heading text=”Related Resource” font_container=”tag:h1|text_align:left” google_fonts=”font_family:Roboto%3A100%2C100italic%2C300%2C300italic%2Cregular%2Citalic%2C500%2C500italic%2C700%2C700italic%2C900%2C900italic|font_style:300%20light%20regular%3A300%3Anormal” tm_text_transform=”uppercase” css=”.vc_custom_1541533930179{padding-top: 10px !important;padding-bottom: 10px !important;}”]

User Presentation

Real-Time Open Data Sharing of Zika Virus Research Using LabKey

The laboratory of David O’Connor at the University of Wisconsin-Madison has been at the forefront of Zika virus research since the disease’s 2015-2016 outbreak in the Americas. The laboratory conducts studies with non-human primates to establish the natural history of infection and create a model that can be used to target future vaccine development. A key component of the lab’s work is the usage of the LabKey Server platform for real-time open data sharing of zika virus data with researchers worldwide and aggregation of diverse types of data that have been contributed by a large group of researchers into a central place.

In this presentation Michael Graham of the O’Connor lab shares how their team partnered with LabKey to provide open access to data during this public health emergency. Watch presentation >

A standard nomenclature is incredibly valuable for teams using LabKey Server to do collaborative biomedical research and becomes increasingly more important as they grow in size and data volume. Defining how data fields should be named is essential to the efficiency of teams, as it aids both those generating and/or capturing data as well as those conducting data analysis.

As you get started using LabKey Server, keep in mind the best practices below for defining and maintaining a standard nomenclature in your lab:

Define Nomenclature Up Front

Standardizing nomenclature may seem like an unnecessary up-front investment, but ultimately your team will experience less confusion and more efficiency as they progress with their work. Empower your team by allowing them to have a voice as you define which terms will be used in your research. By including team members in the process, they will feel more invested and be more likely to adhere to standard naming conventions.

Use LabKey QC Features to Ensure Consistency

In an ideal world, all team members will consistently use the nomenclature agreed upon by the team when adding data to your LabKey Server. But in practical application, it is more likely that from time to time a team member will mistakenly enter “H20” instead of the lab standard name “Water” into their ingredient list, potentially breaking standard reports, grid views, etc.

Using LabKey quality control features like lookups, aliases, and validators in key fields can help combat this scenario. A LabKey lookup will allow you to to map several common variations of a term to a desired standard field value. For example, an administrator could configure a lookup so that “H20” and “Tap Water,” common deviations from the standard, would both map to “Water.” These types of lookups allow teams to maintain the integrity of their data, in spite of inevitable human error.

Administrators can also use to regex or range validators on new data being entered to ensure that users are entering valid data into the system. By placing these restrictions, teams can improve data entry and help analyses down the pipeline.

Evaluate and Adjust

It’s easy to enforce the use of standard nomenclature when your team is small and your research is in its early stages. But over time, as teams grow and become further removed from when nomenclature guidelines were established, they can develop a “laboratory shift” in how things are named. In order to stay on top of your terminology and keep your data clean, plan to regularly review and assess your standard nomenclature. Are there additional terms that need to be defined? Have any standard terms become outdated? Are certain terms consistently being used incorrectly? Making small adjustments as your research needs evolve will help maintain the integrity of your data.

LabKey helps enforce nomenclature standards, leading to cleaner data and more efficient research. Sign-up for a free trial to see these and other core LabKey Server features in action. 

Related Documentation

• Lookup Columns 
• Field Level Validation
• Data Quality Control

Integrated NLP data management solution speeds clinical data abstraction and curation for disease registries, clinical research and quality reporting

Cambridge, England and Seattle, WA, USA — September 25, 2018 — Linguamatics, the leading natural language processing (NLP) text analytics provider, and LabKey, a provider of bioinformatics data management solutions, today announced an integrated solution designed to streamline the extraction and curation of valuable insights from large volumes of unstructured clinical notes and reports.

With Linguamatics NLP engine I2E, healthcare and life sciences teams can significantly reduce the manual processes involved in information analysis and extraction. When integrated with LabKey Server’s document processing pipeline and curation user interface (UI), the combined solution provides an end-to-end pathway for unstructured data from acquisition to analysis.

“Our partnership with LabKey empowers healthcare teams to achieve high accuracy data extraction in a wide variety of use cases” said Simon Beaulah, senior director, healthcare at Linguamatics. “Customers can speed extraction of EHR data into cancer registries and clinical data warehouses; reduce the manual burden associated with clinical study review; and rapidly extract relevant population health data and quality metrics to improve business critical HEDIS quality metrics reporting and patient outcomes.”

The LabKey and Linguamatics relationship is based on collaborative work with the NCI’s Surveillance, Epidemiology, and End Results (SEER) Program. This project has resulted in an NLP pipeline that automates the annotation and review of pathology reports, to build a large gold standard for machine learning training.

“Combining LabKey’s processing pipeline, workflow, and curation UI with Linguamatics’ NLP capabilities provides a complete solution for organizations that need to extract valuable information from large volumes of unstructured clinical data,” explained Adam Rauch, vice president of product management at LabKey. “This integrated system empowers abstractors and reviewers with the technologies they need to accelerate the extraction process from end-to-end.”

About Linguamatics

Linguamatics transforms unstructured big data into big insights to advance human health and wellbeing. A world leader in deploying innovative natural language processing (NLP)-based text mining for high-value knowledge discovery and decision support, Linguamatics’ solutions are used by top commercial, academic and government organizations, including 18 of the top 20 global pharmaceutical companies, the US Food and Drug Administration (FDA) and leading US healthcare organizations.

Linguamatics I2E is used to mine a wide variety of text resources, such as scientific literature, patents, Electronic Health Records (EHRs), clinical trials data, news feeds, social media and proprietary content. I2E can be deployed as an in-house enterprise system, or as Software-as-a-Service (SaaS) on the cloud.

About LabKey

LabKey provides software solutions to help teams overcome the data management and workflow challenges faced in today’s biomedical research environment. LabKey works hand-in-hand with clients to understand the complex needs of modern labs and develop flexible, scalable, extensible systems to address them.

LabKey Server is an open source software platform for integrating biomedical research data and managing laboratory workflows. LabKey Server is highly configurable and is used by research organizations across the globe to provide reliable, scalable environment for research data. [vc_row gap=”30″][vc_column width=”1/2″][vc_column_text css=”.vc_custom_1537808118148{padding: 30px !important;background-color: #ededed !important;}”]

LabKey Media Contact

Kelsey Gibson, Marketing Manager
LabKey

+ 1 425.308.7033
kelseyg@labkey.com[vc_column width=”1/2″][vc_column_text css=”.vc_custom_1537808128682{padding: 30px !important;background-color: #ededed !important;}”]

Linguamatics Media Contact

Michelle Ronan Noteboom, Sr. Account Director
Amendola Communications

+ 1 512.426.2870
mnoteboom@acmarketingpr.com

CAR T and other cellular immunotherapy trials are rapidly expanding worldwide due to their high success rates and continued scientific advancements that are helping generate new therapeutic targets. The development of these advanced immunotherapies requires extensive data collection and collaboration between research scientists, clinical teams, and trial subjects. In order to manage immunotherapy data efficiently and improve the feedback loop from current and ongoing trials many research teams are seeking out secure, web-based data management solutions in lieu of traditional paper based systems to manage their trial data.

LabKey is actively partnering with teams conducting immunotherapy trials to provide LabKey Server-based solutions to overcome a wide variety of challenges and accelerate their research, including:

Integrating Heterogeneous Immunotherapy Data

Cutting edge cellular immunotherapy trials rely on data generated at multiple sources often including the cellular manufacturing facility, the clinic gathering subject data, and research labs exploring the cellular profile of the therapy. Teams conducting CAR T and other immunotherapy trials need reliable software tools to integrate this heterogeneous data and provide a comprehensive view of the therapy’s efficacy and safety to clinicians and researchers.

LabKey Server helps immunotherapy research teams efficiently integrate heterogeneous data by providing:

• A data-aware study module that can recognize and integrate disparate vendor datasets, alias subjects and track visits by name or by date
• Built-in and customizable integration with electronic data capture systems and case report forms

Longitudinal Study Data Capture

Lengthy follow-up periods are typically required for subjects undergoing therapy involving genetically modified cells. Managing trial data over time in a secure and scalable manner quickly becomes very challenging for paper-based systems.

LabKey Server helps support the consistent collection and storage of longitudinal study data throughout the lifetime of a trial by providing:

• A configurable study progress report that allows trial staff to manage samples and tests, ensuring that every result is accounted for.
• The flexibility to customize and modify the system as the needs of the database grow and change, without compromising historic data.
• Professional support and services to ensure that the system is maintained throughout the life of the trial.

Explore this Longitudinal Study in LabKey Server

This example study compares various anti-retroviral (ARVs) treatment regimens by monitoring HIV-1 disease progression in 122 participants.

Compliant Collaboration

Sharing reports and data with collaborators improves research, innovation, and ultimately subject care. Maintaining compliance and having the ability to quickly share data and reports is an important topic to tackle in immunotherapy research where subject safety and care is the top priority.

LabKey Server improves reporting and collaboration amongst collaborators conducting immunotherapy trials by providing:

• Dynamic and static reporting tables and visualizations that can be shared as-needed
• Web-based access to a central platform for data sharing
• The ability to remove PHI fields or provide randomized IDs when sharing
  information with collaborators

[vc_cta h2=”Explore LabKey Server” add_button=”bottom” btn_title=”Start Your Trial” btn_style=”custom” btn_custom_background=”#779e47″ btn_custom_text=”#ffffff” btn_shape=”round” btn_align=”left” btn_link=”url:https%3A%2F%2Fwww.labkey.com%2Ftrial-sign-up%2F|||”]With the right tools, immunotherapy research teams can push the pace of this cutting edge research even further, increasing trial efficiency to bring life saving therapies to more patients faster. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common immunotherapy research challenges.[/vc_cta][vc_custom_heading text=”Related Resource” font_container=”tag:h1|text_align:left” google_fonts=”font_family:Roboto%3A100%2C100italic%2C300%2C300italic%2Cregular%2Citalic%2C500%2C500italic%2C700%2C700italic%2C900%2C900italic|font_style:300%20light%20regular%3A300%3Anormal” tm_text_transform=”uppercase” css=”.vc_custom_1541533930179{padding-top: 10px !important;padding-bottom: 10px !important;}”]

User Presentation

Using Existing LabKey Modules to Build a Platform for Immunotherapy Clinical Trials

The Correlative Studies Laboratory (CSL), part of the Immunotherapy Integration Hub at Seattle Children’s, focuses on understanding how reprogrammed T cells react in each patient in terms of their persistence, functionality and efficiency at reducing tumor burden. This data, combined with manufacturing and clinical data generated during clinical trials, enable researchers to answer pressing questions with minimal time and resource investment.

In this presentation Olivia Finney, shares how the CSL is working with LabKey to integrate, analyze and securely share data in order to create a truly translational research model. Watch presentation >

LabKey Server gives teams the flexibility to assign permissions to individual users or to security groups. While teams are setting up and implementing LabKey Server, assigning user permissions individually often seems like the easiest route, but for growing teams or active labs that strategy can become an administrative challenge in the long run. As your team and/or use of LabKey Server grows, it becomes much easier for administrators to control permissions with User Groups.

What’s more important than which method you choose, is taking the time to define your permissions strategy up front. A defined and documented policy will help make managing security easier to implement and maintain long term. Take a look at the best practices below to set yourself up for success when creating a permissions strategy:

1. Define User Groups

Think about the functional requirements of your team; are there members that will need read-only access and some members that need to enter in data? By splitting out what the needs of each person are, you can easily define user groups based on common access needs.

2. Consider Folder Structure

Take your LabKey Server folder structure into consideration when defining security groups; should your team members have the same permissions to all folders? Do certain team members need the same level of access but to different folders? Use your folder structure to help further segment users into appropriate security groups.

3. Monitor and Adjust

Review and refine user groups over time as the use of LabKey Server continues to grow. Administrators should review their permission settings at a regular frequency to make sure permissions for a User Group are accurate and appropriate for the current situation. Use LabKey Server’s Impersonate feature to view access as each User Group and verify that the permissions assigned to each group are correct.

Get started securely sharing data with team members and collaborators using LabKey Server! Sign-up for a free trial to see LabKey Server permission management features in action.