Category: About LabKey

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