Tag: Server SDMS

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

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

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

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

LabKey for COVID MyStudies

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

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

Related Resources

COVID MyStudies Support Documentation – LabKey

COVID MyStudies Announcement – FDA

Contact the support team at FDAMyStudiesContact@harvardpilgrim.org

Contact FDA at CDERMedicalPolicy-RealWorldEvidence@fda.gov

Data Management in translational research is key to gleaning insights that lead to personalized treatment plans for patients. Translational research has advanced rapidly in recent years, but patient treatment efforts have been hindered by poor data management practices, error-prone manual workflows, and a lack of collaborative spaces where scientists and clinicians can easily share data and analyses.

With the multitude of data sources and types involved in translational research, teams need flexible data management software tools to help maximize insights and knowledge transfer from bench to bedside. LabKey Server provides the essential tools to overcome the unique data management and collaboration challenges posed by interlinking data from research and patient treatment.

Managing Translational Research Data

Proper lab data management in translational research is vital in improving repeatability and reproducibility in experiments. This ultimately leads to more reliable research studies, improved product development and better patient outcomes in a shorter time frame. Data management software plays a central role in managing the integration, quality control, analysis, and sharing of translational research data. In LabKey Server, these features include:

• The ability to seamlessly connect raw assay data with metadata and the original experiment
• Built-in quality control tools for recognizing and handling erroneous values
• A file watcher that automatically loads new data into a new or existing dataset as it becomes available, reducing human interaction and error
• Compliance tools for ensuring data is reviewed and an electronic signature recorded

Comprehensive Data Integration

Translational research involves many scientists and clinicians compiling multiple data types and sources. These may include deidentified patient data, whole genome or exome sequences, specific tumor sequences, specimen records from patient blood draws, biopsies, and more. Without a data integration hub, this is a daunting and time-consuming process that can potentially slow down research and the downstream treatment offered to patients.  LabKey Server includes these powerful features for integrating translational research data:

• A compliant study environment with tools that simplify the integration of clinical and research data
• Automated methods for aligning data from a variety of sources (flow cytometry, Luminex, antibody data, data from electronic data capture systems, etc.)
• Flexibility and simplified methods for collecting ad-hoc results
• Tools for comparing subjects across multiple studies

Collaboration and Sharing of Research Data

Sharing data with collaborators improves accountability, innovation, and ultimately the production of new therapies for patients. Hurdles like institutional firewalls and outdated data-sharing methods, like emails, spreadsheets and insecure websites, often hinder collaboration in the scientific community. LabKey Server helps teams collaborate securely by providing:

• Web-based access to a central platform for data sharing
• A compliant environment with multi-level permissions, so data sharing is secure
• The ability to protect PHI data or randomize IDs when sharing information with collaborators

Case Study: City of Hope

City of Hope is a comprehensive cancer care center treating patients using the Total Cancer Care protocol. LabKey Server brings together clinical and genomic data, making it available across the entire City of Hope enterprise where it can be used to improve precision-based therapies. LabKey Server integrated with their existing data warehouse systems, provided users with graphical access to querying and reporting, as well as API access for developers and users performing more advanced analysis techniques. LabKey also supports City of Hope’s needs for team collaboration solutions, API development, and workflow integration, with an audit system that supports regulatory compliance. 

Read More: LabKey Improves Data Accessibility for Total Cancer Care Protocol at City of Hope

Related Documentation

• Uploading, Integrating and Modeling Instrument Data
• Data Quality Control
• File Watchers – Automated Directory Monitoring
• Longitudinal Study Data Management
• Regulatory Compliance Features
• Security Model- Roles & Permissions

Researchers focusing on COVID-19 are using the LabKey Open Research portal to collaborate and share study data. Teams from the Dave O’Connor and Tom Friedrich labs at the University of Wisconsin have started “The CoVen”– a collaboration and data sharing initiative for researchers across a variety of institutions studying the SARS-CoV-2 virus. The diverse data shared in the portal is derived from both human clinical samples and nonhuman primate models. The CoVen teams are contributing to COVID-19 research by focusing on the following key areas:

• Collaboration on nonhuman primate research studies of the virus. 

Since SARS-CoV-2 causes respiratory disease in infected rhesus macaques and other nonhuman primates, they are a useful animal model for COVID-19.  This includes developing and sharing a Clinical Scoring System and Lab Value Reference Guide to help maintain data consistency across future nonhuman primate COVID-19 studies. Information on animal model development and links to COVID-19 animal model preprints are also made available for reference and exploration

• Conducting longitudinal viral genome sequencing from human isolates to understand virus evolution.

Viral RNA sequencing from human isolates gives insight into the transmission chain from person to person, and how it differs from city to city.

• Optimizing assays for virus and antibody detection in nonhuman primate and human clinical samples. 

The development of assays to rapidly detect infections is essential in curtailing the pandemic. The O’Connor Lab is developing assays to detect COVID-19 viral nucleic acids in swab samples to detect current infections, as well as detect antibodies targeting SARS-CoV-2 in serology samples to determine if someone has been previously exposed and mounted an immune response.

LabKey Open Research Portal for COVID-19 Collaboration

Built using LabKey Server, the LabKey Open Research portal helps CoVen researchers directly coordinate with collaborators to post real-time updates and monitor the progress of ongoing studies. The portal provides a platform that facilitates communication, data uploads, and efficient tracking of updates. These real-time updates allow the CoVen team to fine tune study designs and discuss future directions of studies based on data from each site.

By sharing real-time study updates on the portal, research teams from around the world have accessed the data. This has facilitated further collaboration and helped the CoVen team to learn from other research studies, share and develop standardized clinical scoring criteria, PET/CT imaging techniques, virological and immunological assays, and study designs.

Open Research Portal projects are freely available to researchers. If you are interested in sharing real-time data through the portal, please contact us.

The LabKey Server platform can be easily configured to manage longitudinal study data allowing for efficient curation, analysis and publishing. These features include data integration, a customizable study framework, quality control workflows, an intuitive visualization builder, manuscript development tools, and de-identified data publishing. 

To help users configure LabKey server to their study data needs as well as to help those evaluating LabKey, we have put together a series of tutorials. You can also try LabKey server using these resources:

>Explore an Example Research Study 

>Start a Trial of LabKey Server

>Design Your Own Study

Research Studies with LabKey Server 

Interactive Data Grids
The LabKey platform provides a graphical user interface to import, query and analyze your research data. Learn how easy it is to chart, correlate, and drill down into your data in this quick online tour.

Time Chart Visualizations
Visually presenting research data in a way that your users can easily answer their own questions can bring your results to life. In a LabKey time chart, the user can change how the underlying data is shown while the live underlying data updates continuously behind the scenes.  In this visualization you can experiment by checking the grouping boxes of the time chart. If you click ‘Edit’ and then ‘Chart Type’ you can access the Plot and Chart Builder to see other data in other ways.

Plot and Chart Builder
In the common plot editor, you can change the type and layout of a chart. On this example, click ‘Chart Type’ to select another plot type, change what data is shown using drag and drop, and use color and shape to add more information. To learn more about building meaningful visualizations within a study see this tutorial- Tutorial: Longitudinal Studies

Quality Control
Tracking the quality of data involves various control measures. LabKey studies can integrate QC status and easily filter to identify approved data as well as data that is in need of further attention. You can see a filtered set of data that has not yet been reviewed by clicking here.

Secure Access
Sharing reports and data with collaborators improves research, innovation, and ultimately patient care.  Protecting the same information from outside access is vital in maintaining patient privacy. Using a trial server, you can use this tutorial to create a working model to see how role and group based access works.

Precision medicine for the treatment of cancer involves integrating, aligning and providing access to a multitude of data types. This includes patient data, whole genome or exome sequences, specific tumor sequences, specimen records from dozens of blood draws, biopsies, and more. A recently published case study outlines how LabKey Server provides data integration, analysis and collaboration tools to City of Hope as they treat patients using the Total Cancer Care Protocol. Working within the Oncology Research Information Exchange Network (ORIEN) consortium, the goal of this project is to bring together clinical and genomic data, making it available across the entire City of Hope enterprise where it can be used to improve precision-based therapies.

LabKey at City of Hope

LabKey Server integrates with existing data warehouse systems at City of Hope, provides users with graphical access to querying and reporting, as well as API access for developers and users performing more advanced analysis techniques. There are two main components to how City of Hope is using LabKey Server:

1. Data aggregation from disparate sources and alignment with patient information
2. Management of the workflow process itself, including automated import and scripted transformation of data.

More than just a software vendor, LabKey also supports City of Hope’s needs for team collaboration solutions, API development, and workflow integration, with an audit system that supports regulatory compliance. Looking ahead, LabKey solutions offer the expansion and flexibility required for scaling the City of Hope and ORIEN networks into broader use.

Additional Information

Case Study: LabKey Server at City of Hope

LabKey User Conference Presentation: Watch Video

Request a demo of LabKey Server

Google Cloud recently announced that they are working to expand FDA MyStudies, an open-source technology platform that supports research organizations as they collect and report real-world data for regulatory submissions. LabKey provides the backend data management for FDA my studies via a dispersed data model that securely partitions personally identifying information to help ensure patient privacy.

With Google Cloud, organizations will now have another alternative to securely host their deployment of MyStudies. This secure hosting provides organizations with safeguards in the ownership and management of data in their studies including the ability to select which of its researchers and clinicians are able to access what data, and to help optimize the use of that data as directed by participants.

In developing the FDA MyStudies platform, LabKey Server was selected as the data management partner due to its flexible open architecture and ability to securely handle personal health information in a compliant manner. LabKey Server also provides role-based governance of the data stored on the Registration and Response servers to ensure that data is only accessible to authorized users. 

At LabKey, we are excited to learn about the integration with Google Cloud and look forward to having an additional option for secure hosting of the FDA MyStudies platform.  

Additional Resource:
Case Study – FDA MyStudies Mobile App

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.

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

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.

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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.

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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.

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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.

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