Tag: Server SDMS

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 

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

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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 >