Category: LabKey Server

Stay up to date with the latest news about LabKey Server, our open source software platform for data management, scientific workflows, and research data sharing.

20 Nov 2018
New features added to LabKey Server v18.3 for scientific data integration and analysis

What’s New in LabKey Server v18.3

We are excited to announce the release of LabKey Server v18.3! This release includes a variety of enhancements designed to make integration and analysis of data more efficient and secure, including:

  • Support for multiple R engines for a single site. Users can now select an alternative to the default R engine for individual projects as well as declare an R engine as a sandbox environment, isolating it for security purposes.
  • Integration with RStudio Pro* allows users to view, edit, and export LabKey Server data in the RStudio Pro interface.
  • Navigation improvements have been made to project and custom menus to help improve the user experience.
  • Antivirus scanning* automatically checks all file uploads, attachments, archives and other content for viruses during import.
  • Enhancements to visualization tools allow users to specify multiple y axes for scatter and line plots, hide trend lines and data points on time charts, and include visualizations in study participant views.
  • Additional QC Trend reports* including Moving Range and Cumulative Sum plots have been made available for GPAT/file-based assays.
  • ETL definition editor enhancements* provide automatic code completion and allow administrators to define a new ETL using an existing definition as a template.
  • Support for Java 11 allows LabKey to run on both Oracle Java SE 11 and Oracle OpenJDK 11.*

Check out the 18.3 Release Notes for the full list of enhancements included in this release!

Download LabKey Server v18.3 >

*Premium feature, please contact your LabKey account manager for additional information and configuration support. If you’re interested in learning more about premium subscriptions, please contact us.

**Oracle Java SE 8 is supported as well, but will be removed in 19.1.

16 Nov 2018
Java release cadence, LabKey Server

The Java Shake-Up: What it Means to LabKey and You

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 ReleaseJava Versions SupportedChanges
18.3 – Nov 2018Java 11, Oracle Java SE 8Add Java 11
19.1 – Mar 2019Java 11 & 12Add Java 12, Remove Java 8
19.2 – Jul 2019Java 12Remove Java 11
19.3 – Nov 2019Java 12 & 13Add 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

06 Nov 2018
Data sharing platform for infectious disease collaboration

Built for Science: Data Sharing in Emerging Infectious Disease Research

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 platform to help overcome key collaboration challenges, including:

how to integrate heterogeneous data in infectious disease researchIntegrating 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

adaptable database software for infectious disease researchCreating 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

Data sharing software infectious disease researchReal-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

 

Explore LabKey Server

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.

Related Resource

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 >

17 Oct 2018
Using look ups to standardize laboratory nomenclature and clean data entry

Setting Yourself Up for Success: 3 Best Practices for Using Standard Nomenclature

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 standard nomenclature for scientific research up front.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 lookups in LabKey helps standardize the nomenclature used in your research data.

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.

Regularly evaluate and refine the standard nomenclature you use in your scientific research.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

25 Sep 2018
LabKey and Linguamtics partner to speed Natural Language Processing of Clinical and Unstructured Documents

LabKey and Linguamatics Partner to Extract Clinical Insights from Big Data in Healthcare

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 Natural Language Processing NLP Solutions for Healthcare and Life Sciences

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. 

LabKey Media Contact

Kelsey Gibson, Marketing Manager
LabKey

+ 1 425.308.7033
kelseyg@labkey.com

Linguamatics Media Contact

Michelle Ronan Noteboom, Sr. Account Director
Amendola Communications

+ 1 512.426.2870
mnoteboom@acmarketingpr.com

29 Aug 2018
Using security groups to manage access to scientific research data in LabKey Server

Setting Yourself Up for Success: 3 Best Practices for Managing Permissions

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:

Using security groups to manage access to scientific research data in LabKey Server1. 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.

Use a folder structure for organizing scientific research data that supports security in LabKey Server2. 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.

Regularly review LabKey Server security setting3. 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. 

09 Aug 2018
LabKey software tools for clinical research data

Clinical Research: Improving Data Management & Reporting

Managing and reporting clinical data has historically included manual curation and compilation of datasets from disparate data warehouses. In today’s data-rich environment, manual processing and integration is becoming more and more of a bottleneck.

In order to keep up with the increasing amount of data collected from clinical research, clinicians and statisticians alike need software tools that will centralize their data and help them quickly recognize errors. LabKey Server provides essential tools to overcome these, and other key clinical research challenges including:

LabKey tools for maintaining data integrity in clinical research

Maintaining Data Integrity

Having an accurate representation of clinical data helps transform discoveries and understanding into patient care and treatment. Centrally-housing data in a compliant environment that enforces data standardization can help clinicians maintain excellent data integrity and provide an authoritative view of their data landscape.

LabKey Server helps maintain data integrity by providing:

  • A highly structured data environment with enforceable data fields to ensure data is entered correctly and within range
  • Quality control measures such as data flags, QC of datasets and built-in QC reports
  • Role and group-based permission levels that allow users only access to what they need access to
  • A compliance module, the allows users to set PHI securities, set Terms of Use for users, and provide electronic signatures on data snapshots

LabKey tools for integrating clinical research dataIntegration of Data from Multiple Sources

Bringing together data from disparate sources into a single system can help clinical research stay on track and on time. Collaborative monitoring of data quality by clinicians, statisticians, and scientists enables quick identification of erroneous data and ensures a reliable, integrated data landscape for comprehensive data analysis.

LabKey Server helps facilitate comprehensive data integration by providing:

  • A study module that can recognize and integrate disparate vendor datasets
  • Built-in and customizable integration with electronic data capture systems and case report forms
  • A clinical document abstraction pipeline, which can extract valuable data from legacy documents

LabKey tools for secure reporting and collaboration in clinical researchSecure Reporting and Collaboration

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

LabKey Server improves reporting and collaboration 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

With the right tools, clinical research teams can eliminate data integration bottle necks and curate reliable datasets for analysis. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common clinical research challenges.

Related Documentation

Read more about the features highlighted above on the LabKey Support Portal:

11 Jul 2018
LabKey Server software tools for bench-to-bedside translational research

Bench-to-Bedside: Improving the Feedback Loop

Translational research is making large strides in developing and improving effective agents and therapeutic strategies for patients. Despite these advances, bench-to-bedside and then back to bench science is often hindered by poor data management practices, error-prone manual workflows, and a lack of shared spaces where scientists and clinicians can easily collaborate.

In order to be effective in today’s data-rich research environment, teams need effective software tools to help facilitate the feedback loop between the bench and the bedside. LabKey Server provides essential tools to overcome key bench-to-bedside challenges, including:

LabKey software helps maintain good research recordsMaintenance of Good Research Records

Maintenance of good laboratory records is vital for any research and improves repeatability and reproducibility in experiments.  In translational research, this ultimately leads to improved product development, bringing better treatments from bench to bedside faster.

LabKey Server helps teams maintain good research records by providing:

  • The ability to upload raw assay data and assign metadata, allowing experimental data to be traced back to the original experiment
  • Built-in quality control tools that allow scientists to upload their data and examine it for 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, and freeing up time for scientists to focus on the science
  • Compliance tools for signing off on records, ensuring data is reviewed

Integrate laboratory data sources using LabKey software tools

Comprehensive Data Integration

In order to examine the subject comprehensively during treatment, many scientists and clinicians must compile data from multiple sources. This is often time-consuming and slows down research to find better curative agents and therapies.

LabKey Server helps facilitate comprehensive data integration by providing:

  • A compliant study environment with tools that simplify the integration of clinic and research data
  • Automated methods for integrating data from a variety of sources (Flow Cytometry, Luminex, data from Electronic Data Capture systems, etc.)
  • Simplified methods for collecting ad-hoc results
  • Tools for comparing subjects across multiple studies

LabKey software tools for sharing scientific data onlineCollaborative Data Sharing

Sharing data with collaborators improves research, innovation, and ultimately the production of new therapies to help patients. While collaborative data sharing provides significant value in research, hurdles like institutional firewalls and outdated data-sharing methods, like bulky emails 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 remove PHI fields or randomize IDs when sharing information with collaborators

With the right tools, teams can significantly accelerate the pace of translational research. Sign-up for a free trial to see how LabKey Server can help your team overcome these, and other common research challenges.

Try It Now

The trial version of LabKey Server provides access to many of the platform’s core capabilities, in an easy-to-use hosted environment. Users can explore an example project pre-populated with sample data or create and configure their own LabKey projects according to their research needs.

31 Jan 2018

Two Key Things Your Spreadsheet-Based Research Data Management Strategy is Lacking

High-throughput analysis techniques are incredibly powerful and provide teams with more data than ever. While that depth of data often holds the key to scientific insights, organizing such large quantities of data in a consistent and discoverable way has become a major challenge for research teams.

Many teams rely on spreadsheet-based systems to organize and manage their data. This approach becomes less-effective as research scales because spreadsheet-based strategies lack two essential characteristics:

1. Consistency

Spreadsheet data management lacks consistencyManual file management relies on the individual contributor’s abilities to consistently create, name, and store data files. This opens the door to a wide range of human errors that will ultimately impact the discoverability and reliability of your data. Common consistency errors that result from manual data management include:

  • Poorly named files
  • Inconsistent locations
  • Duplicate files

2. Discoverability

Spreadsheet data management lacks discoverabilityCollecting data is a giant hurdle in research, but in reality, it is just the first of many. Researchers need to be able to locate datasets of interest in order to conduct analysis. In a file based environment, discoverability of files is dependent on the consistency with which they are maintained. Were they saved in the correct location? Have they been named according to an agreed upon convention? Is there a clear authoritative file or are there duplicates?

A hitch in any one of these areas can severely hinder the discoverability of your data and make it significantly more difficult to:

  • Track what research data has already been collected
  • Find the data you are looking for when it comes time to analyze

Biology-Aware Data Management with LabKey Server

Scientific data management systems like LabKey Server, help increase the consistency and discoverability of your research data. LabKey Server increases the consistency of data management by providing structured data grids for storing various type of research data. Each data grid type also captures relevant metadata, specific to that data type, in order to help make data more discoverable.

Research-Centric Data Structures

Unlike spreadsheets that treat all types of data the same, LabKey Server provides four primary data structures with unique features to better support common types of research data.*

LabKey Assays – Assay data grids capture data generated from individual experiment runs. Assay data is automatically structured in a batch-run-results hierarchy when data files are added. LabKey Server supports data a variety of common assay designs out of the box, but teams can also design their own assay data structure using LabKey’s General Purpose Assay Design.

LabKey Datasets – Datasets track patient/subject measurements over time. LabKey datasets are automatically aligned and joined together, making it easy to query the integrated data and to create visualizations from multiple datasets.

LabKey Specimens – Specimen repositories track the status of each specimen and vial in your inventory. Built-in reports provide a birds-eye view of specimen information, and advanced search capabilities allow for easy location of specimens.

LabKey Lists – LabKey lists provide general purpose, online, interactive grids for any tabular data. Data stored as a LabKey list can be sorted, filtered, and visualized using built-in tools.

Storing data in a consistent, structured manner is the key for teams that hope to achieve maximum efficiency in operations and maximum value from their data. Not only is it much simpler to find data when it is stored in an expected location, but the centralization and integration makes it possible to query data to more quickly locate information of interest.

Interested in learning more about how LabKey Server can increase consistency and discoverability of your research? Contact the LabKey team for more information or request a demo!

*To learn how to add data to LabKey Server, read documentation >

21 Nov 2017

What’s New in LabKey Server v17.3

We are excited to announce the release of LabKey Server v17.3! This release marks the launch of our newly redesigned user interface and includes a wide variety of other key feature and security enhancements.

Feature Highlights of Version 17.3

User Interface Update

The 17.3 release includes big improvements to the LabKey Server user interface. Enhancements include:

  • Project Navigation – Project and folder navigation has been redesigned as a single-column scrollable list, which also works well on tablets and other small windows. (docs)
  • Frameless Web Parts – You now have the option to render cleaner looking pages using “frameless” web parts, which removes the web part title, the surrounding border, and the top banner. (docs)
  • Grid Interface – Improvements include: (1) new graphics and buttons, (2) filters and sorts are automatically included when saving a custom view, and (3) when saved views exceed 10 items, a text-based filtering box makes it easier to locate the relevant views. (docs)

Electronic Signatures
Electronically sign a data grid snapshot, and specify a reason for signing. Signed documents and associated metadata, such as the signatory, the date of signing, etc. are extensively logged for auditing purposes. (docs)

REDCap Improvements
REDCap integration has been updated and enhanced, including a new graphical user interface which replaces the XML-based configuration interface, making it easier to configure connections and data export from REDCap servers. (docs)

For details on all the new features, read the release notes on the LabKey Support Portal, or download the latest version of LabKey Server.

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