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.

25 Sep 2018

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.

19 Sep 2017

Before & After: A Side-by-Side Look at the New LabKey Server UI

The upcoming redesign of the LabKey Server user interface includes a variety of updates; some of which are focused on look and feel, some on interface behavior, and some technical stability. All of these changes and enhancements were carefully selected because of the contribution they will make to the overall usability of the platform. Prior to the release of the new UI as part of LabKey Server v17.3, we wanted to give users a side-by-side look at some of the key updates and how they will differ from the current UI.

Landing Page

Many of the key changes to the LabKey Server UI can be seen upon your arrival on the LabKey Server landing pages. The new interface features an updated header style with a more compact navigation and reorganized menus, the addition of a new “frameless” webpart style, and updated logic that will hide the tab bar on home projects if there is only one tab present.

Page Administration

In order to reduce the visual noise and present a cleaner UI for administrators, we have introduced a “page admin mode.” Options like “add web part” and tab editing will no longer be presented at all times and will instead only be visible when the user turns on page admin mode. Page admin mode can be easily turned on when edits to a page are needed and turned off when edits are complete.

Data Grids

Several changes have been made to the LabKey data grids in order to declutter the grid navigation and increase readability. The most notable changes include the introduction of a more icon-driven button bar with tooltips for each action available on hover, a simplified “edit” link presentation, and the addition of row highlighting.

Grid Customization

The customizing grids of data has been simplified in the new LabKey Server UI. With this update, filters and sorts added to a grid are always carried with view and no longer require an opt-in. Additionally, filters can be quickly edited using one click to reopen the filter pane or removed with by clicking the newly added [x] icon next to each filter definition.

Menus

Updates to the LabKey Server menu are both visual and technical in nature. A major shift included as part of the redesign is the transition to menus written in Bootstrap instead of Ext, that take advantage of Bootstrap’s consistent styling and built-in behavior for multiple form factors. Sub-menu behavior has also been updated so that sub-menus now replace the menu content (with a back to menu option) instead of appearing next to the primary menu. This change makes the navigating to 2nd level sub menus a much cleaner experience, as users navigate within one menu frame instead of 3. Finally, type-to-filter functionality has been added to the menus with greater than 10 values. This can initially be seen in the “More Modules” list as well as the “Grid Views” list.

12 Sep 2017

Key Steps for a Successful UI Transition

Whether you’re implementing a brand new software solution or updating an existing solution, changes that affect the workflow of team members are often a major pain point for organizations. Taking steps to manage and communicate these changes and their benefits to your users can greatly reduce the friction faced during implementation and, in turn, increase adoption by users. As you prepare to transition to the new LabKey Server UI (being released as part of LabKey Server v17.3), we encourage you to take the following steps to help manage this change and help make the UI transition a success.

Test the Redesigned Interface

Test the new interface extensively in your staging and/or test environments. As part of the 17.2 release of LabKey Server, we included the “Core UI Migration” experimental feature that allows administrators to turn on the new UI. While the interface is still in active development and certain elements may shift slightly, the bulk of the navigation changes are represented, and we encourage administrators to explore the new UI and test for:

Changes to your primary user workflows (editors, readers, administrators, etc.)
Go through the workflows of your primary users; click through the available buttons and navigate through the interface as your user would, checking for changes to their standard workflows.

Broken customizations
Check to see that customizations you have made to the interface are still functioning as expected. As part of the UI redesign, we have refactored a good portion of our own CSS in order to make it easier to maintain the platform in the long run. As a result customizations made to your server’s CSS may need updating.

UI bugs that should be reported to LabKey
Reporting bugs that you encounter during testing is an important part of the redesign process. Your feedback helps us identify and prioritize fixes that need to be made to the interface.

Identifying updates that need to be made to your server customizations and changes to your user workflows early will give you the opportunity to make adjustments and prepare for any new-interface training that might need to be done with users.

Set a Go Live Date

Decide on a date that you will make the transition to the new UI. Make sure you account for adequate time to test the new version, communicate upcoming changes and your transition plan, and train users on the new UI.

Communicate Upcoming Changes and Transition Plan

Communicating upcoming changes and their implications for your users early and often is crucial to a smooth interface transition. When communicating details about the interface transition to users, make sure to include information about:

  • Transition timeline
  • Key benefits of the transition
  • Key changes/potential areas of frustration
  • How users can ask questions
  • How users can provide feedback

Provide User Training

Some of the changes being made to the LabKey Server interface during this redesign will affect how users perform certain tasks. If you discover through testing the interface in the context of your team’s key workflows that core tasks are affected by navigation changes, then providing training on how to accomplish this work in the new interface will help avoid frustration. For smaller changes, simply documenting the new process may be sufficient training, but in cases where a user’s workflow is significantly changed a training session may be more appropriate.

Answer Questions

Even with thorough testing, communication, and training, questions from your users are still inevitable. Develop and communicate how users can ask questions as they are are adjusting to the redesigned interface. Depending on the size of your team, that may mean communicating who the contact person is for questions, you may create a message board for questions and discussion, or you may host a handful of Q&A workshop sessions post-implementation. Whatever the method, making sure a user knows how they can have their questions answered will help prevent frustration when they encounter a change to their workflow.

Provide Feedback

Communicating feedback to the LabKey team is an essential part of the redesign process, and we are committed to making sure that you and your users have the best possible experience using LabKey Server. As you explore the redesigned interface in your test environment as an experimental feature, you can provide feedback using the “Give Feedback” button in the top right corner of the interface. You can also provide feedback directly to your LabKey account manager.

Related Resources

01 Aug 2017

FAQs: LabKey Server Redesign

In the 17.2 release of LabKey Server, we included an experimental feature that allows teams to explore the beta version of the redesigned LabKey Server UI (scheduled for full release as part of v17.3). The key priorities for this redesign are to transition the platform to using modern technologies that will increase its stability and ease of use, and to respond to user feedback about areas of the platform that needed to be reworked to better support today’s users.

As you explore the new UI, we encourage you to provide feedback about the design and any technical bugs you come across. This will help us make adjustments during the next few months of active development before the initial release. Below are the answers to some common questions you may have when testing the new UI on your LabKey Server. We will continue to add to this list as we receive additional feedback.

Do we have to transition to the new interface or can I keep using the old one?

In 17.2, you’ll have the option to turn on the new look and feel by going to the experimental features listed under the Admin Console and enabling “Core UI Migration.” This will be opt-in, but we recommend you take a look now and provide feedback!

Since this turns the new interface on for all users, and this is still undergoing significant development, we recommend that you turn this on first on your test and/or staging server(s) and not yet on production.

With the 17.3 release, all installs will be moved to the new interface and the old UI will no longer be available for use.

What will happen to my custom CSS when we switch to the new UI?

To support the redesigned UI we are utilizing the standard Bootstrap framework and refactoring a good portion of our own CSS in order to make it easier to maintain the platform in the long run. It is likely that your custom CSS will need updating as a result of these changes.

We recommend that you move your staging server over to the new UI as soon as possible in order to evaluate and update any custom CSS that does not render correctly in the interface. If you are a Premium Edition client, contact your LabKey account manager if you need support making these changes.

Why does my site logo look broken?

By default, the 17.2 release uses the Seattle theme, which has a dark blue bar at the top of the header. Logos that use transparency may look wrong if they were previously on a white background. To fix this, you either upload an alternate version of your logo that will render well on dark background or you can switch to the Seattle Light theme which has a white top bar by going to Admin Console and adjusting your Look and Feel Settings.

Can I change the colors used in the interface?

In the beta release of the interface with v17.2, there are two default theme options to choose from: Seattle and Seattle Light. With 17.3, we expect to have the full suite of themes available for use, with a light and dark version of each. Additionally, you will still have the option of writing custom CSS.

We plan to introduce additional customization options as part of future releases that will allow you to more easily change change specific variables without writing your own CSS.

How do I add webparts to my pages in the new UI?

In order to streamline our page controls, we decided to make those that are used less often only show up conditionally. Most of our administrative controls are now available only when you go into admin editing mode. To turn this on, you can go to the admin dropdown and select “Page Admin Mode” (provided you have administrator permissions):

LabKey Server Page Admin ModeWhile this editing mode is on, you have the ability to add, move, or remove webparts and adjust page tabs just as you did in the previous versions. You can exit this mode by clicking on “Exit admin mode” in the header or in the admin dropdown.

LabKey Server Exit Admin Mode

I found a bug with the new UI. How do I report it?

You can report bugs using the “Give Feedback” link in the top right corner of the new UI. This link will redirect you to a feedback form on the LabKey Support Portal where you can report issues as well as general feedback. Please provide clear steps on how to reproduce bugs you encounter so that we can appropriately investigate and prioritize changes to be implemented in the 17.3 release and beyond.

I use ExtJS 4.x in my applications, why does my view not show up in the new UI?

With the introduction of the new UI we were able to move away from ExtJS 4.x for rendering menus. This was the last “site-wide” dependency we had on ExtJS, however, we still continue to use it throughout the product in different views, reports, and dialogs. To manage these usages we use our dependency framework to ensure the correct resources are on the page. The framework provides a variety of mechanisms for module-based views, JavaServer Pages, and Java.

If your applications do not declare their dependencies, it is likely they will fail to load when they are loaded independently (without other views/apps on the page that might be declare the same dependencies).

14 Jul 2017

What’s New in LabKey Server v17.2

We are excited to announce the release of LabKey Server v17.2! This release includes valuable enhancements to platform features and performance improvements including:

For a complete list of updates and enhancements included in LabKey Server v17.2, check out the release notes.

Download LabKey Server v17.2 >

*Premium feature, please contact your LabKey account manager for additional information and configuration support.

LabKey Server Gets a Refresh

Also included in the LabKey Server v17.2 release is an experimental feature allowing administrators to explore the beta version of the redesigned LabKey Server user interface (scheduled for full release November 2017). We encourage administrators to explore the in-development UI in their dev/test environments and provide feedback prior to the full release.

Learn more about the UI refresh >

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