Getting Started

• Tutorials - Tutorials for new users.
• Videos - Video resources for beginners and experts.
• Install LabKey Server (Quick Install) - Install LabKey Server with a graphical installer.
• LabKey Terminology/Glossary - Definitions for common terms in LabKey Server.

Documentation Contents

• Data Basics - Build applications from user interface panels and views on underlying data.
• Laboratory Data - Work with instrument-derived data.
• Research Studies - Integrate heterogeneous data in longitudinal/cohort studies.
• Collaboration - Set up file repositories, message boards, and issue trackers.
• Development - Developer resources.
• Administration - Create projects, configure security, advanced installation.
• Products and Services - LabKey Server products and services.

Documentation Highlights

• What's New in 17.1 - Highlighted features in the 17.1 release.
• Release Notes 17.1 - Detailed feature list.
• Upcoming Features in 17.2 - Features in development for the 17.2 release.

This topic is for absolute beginners to LabKey Server. It explains what LabKey Server is for, how it works, and how to build solutions using its many features.

What is LabKey Server?

LabKey Server's features can be grouped into three main areas:

1. Data Repository

LabKey Server lets you bring data together from multiple sources into one repository. These sources can be physically separated in different systems, such as data in Excel spreadsheets, different databases, FreezerPro, REDCap, etc. Or the data sources can be separated "morphologically", having different shapes. For example, patient questionnaires, instrument-derived assay data, medical histories, and specimen inventories all have different data shapes, with different columns names and different data types. LabKey Server can bring all of this data together to form one integrated whole that you can browse and analyze together.

2. Data Showcase

LabKey Server lets you securely present and highlight data over the web. You can present different profiles of your data to to different audiences. One profile can be shown to the general public with no restrictions, while another profile can be privately shared with selected individual colleagues. LabKey Server lets you collaborate with geographically separated teams, or with your own internal team members. In short, LabKey Server lets you create different relationships between data and audiences, where some data is for general viewing, other data is for peer review, and yet other data is for group editing and development.

3. Electronic Laboratory

LabKey Server provides many options for analyzing and inquiring into data. Like a physical lab that inquires into materials and natural systems, LabKey Server makes data itself the object of inquiry. This side of LabKey Server helps you craft reports and visualizations, confirm hypotheses, and generally provide new insights into your data, insights that wouldn't be possible when the data is separated in different systems and invisible to other collaborators.

The LabKey Server Platform

LabKey Server is a software platform, as opposed to an application. Applications have fixed use cases targeted on a relatively narrow set of problems. As a platform, LabKey Server is different: it has no fixed use cases, instead it provides a broad range of tools that you configure to build your own solutions. In this respect, LabKey Server is more like a car parts warehouse and not like any particular car. Building solutions with LabKey Server is like building new cars using the car parts provided. To build new solutions you assemble and connect different panels and analytic tools to create data dashboards and workflows.

The following illustration shows how LabKey Server takes in different varieties of data, transforms into reports and insights, and presents them to different audiences.

How Does LabKey Server Work?

LabKey Server is a web server, and all web servers are request-response machines: they take in requests over the web (typically as URLs through a web browser) and then craft responses which are displayed to the user.

Modules

Modules are the main functionaries in the server. Modules interpret requests, craft responses, contain all of the web parts, and application logic. The responses can take many different forms:

• a web page in a browser
• an interactive grid of data
• a report or visualization of underlying data
• a file download
• a long-running calculation or algorithm

• PostgreSQL
• MS SQL Server
• Oracle
• My SQL
• SAS

The illustration below shows the relationships between web browsers, LabKey Server, and the underlying databases. The modules shown are not a complete set; many other modules are included in LabKey Server.

User Interface

You configure your own user interface by adding panels, aka "web parts", each with a specific purpose in mind. Some example web parts:

• The Wiki web part displays text and images to explain your research goals and provide context for your audience. (The topic you are reading right now is displayed in a Wiki web part.)
• The Files web part provides an area to upload, download, and share files will colleagues.
• The Query web part displays interactive grids of data.
• The Report web part displays the results of an R or JS based visualization.

The illustration below shows a data dashboard formed from tabs and web parts.

Folders and Projects

Folders are the "blank canvases" of LabKey Server, the workspaces where you organize dashboards and web parts. Folders are also important in terms of securing your data, since you grant access to audience members on a folder-by-folder basis. Projects are top level folders: they function like folders, but have a wider scope. Projects also form the center of configuration inside the server, since any setting made inside a project cascades into the sub-folders by default.

Security

LabKey uses "role-based" security to control who has access to data. You assign roles, or "powers", to each user who visits your server. Their role determines how much they can see and do with the data. The available roles include: Administrator (they can see and do everything), Editors, Readers, Submitters, and others. Security is very flexible in LabKey Server. Any security configuration you can imagine can be realized: whether you want only a few select individual to see your data, or if you want the whole world to see your data.

The server also has extensive audit logs built. The audit logs record:

• Who has logged in and when
• Changes to a data record
• Queries performed against the database
• Server configuration changes
• File upload and dowload events
• And many other activities

The Basic Workflow: From Data Import to Reports

To build solutions with LabKey Server, follow this basic workflow: import or synchronize your data, apply analysis tools and build reports on top of the data, and finally share your results with different audiences. Along the way you will add different web parts and modules as needed. To learn the basic steps, start with the tutorials, which provide step-by-step instructions for mastering the basic building blocks available in the server.

Ready to See More?

• You don't need to download or install anything to try a few basic features right now: Data Grid Tutorial.
• To further explore LabKey Server, install the server on your local machine, and try a step-by-step tutorial.

• Securely share your data with colleagues through interactive grid views
• Collaboratively build and explore interactive visualizations
• Drill down into de-identified data for study participants
• Combine related datasets using data integration tools

Assay Instruments and File Types

Research and Lab Software

Databases

Authentication Software

LabKey provides software solutions to help researchers overcome the data management and workflow challenges faced in today’s biomedical research environment. Whether you are developing data-driven treatment plans for patients, optimizing processes for more efficient drug development or exploring integrated data to uncover trends in disease, LabKey solutions provide the tools you need to turn data into discovery.

• Academic Research: Adaptable solutions that enable academic researchers to focus on discovery, not data management.
• Pharma & Biotech: Seamlessly integrate data into a secure, central repository for cross-project analysis and optimize processes with flexible, automated workflows.
• Clinical & Provider: Researchers and physicians can access integrated data in a compliant environment with a full suite of tools to expose disease trends and make data-driven treatment decisions.

The breadth of academic research is endless and constantly evolving. LabKey Server offers a wide range of solutions and tools that can be configured to the unique requirements of any scientific research organization. The common thread is diverse sets of tabular data to which you will apply analysis and derive insight.

To get started, explore some ways to work with data using our samples and scenarios. Get inspired about how you can apply them to your own projects.

Getting Started

• 10 Minute Tour - Try the basics of working with tabular data in LabKey Server.
• System Integration: Instruments and Software - Explore a directory of instruments and systems our users are already using with LabKey.
• Reports and Visualizations - Built in visualizations and charts unlock insights for sharing.

Documentation

• Collaboration - Work together effectively with colleagues.
• Data Basics - LabKey offers a scalable way to bring 'spreadsheets' to life in research science.
• R Reports - Integrate statistical analysis using R.
• More Documentation

Tutorials

• Tutorial: Security - Learn how to organize projects and ensure only appropriate access to your private data.
• Tutorial: Cohort Studies - Integrate and analyze observational study data.
• More Tutorials

Additional Resources

• Products and Services - LabKey Server Products and Services.
• LabKey Terminology/Glossary - Definitions for common terms in LabKey Server.
• FAQ - Frequently Asked Questions

Rapid innovation drives progress in the biotech and pharmaceutical industries and you need tools that evolve as fast as your research. LabKey provides the flexibility of a custom tool without the risk of starting from scratch. Seamlessly integrate data into a secure, central repository for cross-project analysis and optimize processes with flexible, automate workflows.

Centralize Data Securely

Integrate high volumes of data from diverse systems into a secure centralized repository.

• Laboratory Data
• Security

Achieve Faster, More Reliable Processes

Automate workflows and standardize processes, review and refine to achieve maximum efficiency.

• Collaboration
• Genomics Workflows

Enable Aggregated Data Analysis

Analyze your complete data landscape, conducting queries and visualizations using LabKey tools or external analysis packages.

• Reports and Visualizations
• Sample Sets

Facilitate Cross-Project Collaboration

Extend the use of data by making it available to collaborators in a secure, web-based environment.

• Proteomics
• Publish a Study: Protected Health Information

Your data has the power to fuel better results for patients, but without proper management, harnessing that power can be a challenge. LabKey Clinical & Provider solutions provide researchers and physicians access to integrated data in a compliant environment with a full suite of tools to expose trends in disease and make data-driven treatment decisions.

Achieve Maximum Visibility Through Integration

Bring together high volumes of data from multiple locations and instruments to create an integrated data picture.

• Electronic Data Capture (EDC) - Replace a paper process with a reliable electronic format.
• System Integration: Instruments and Software - LabKey supports many different instruments out of the box and can be customized to support more.

Have Confidence in Compliance

Create a security and audit framework to ensure consistent compliance with regulatory standards.

Distill Data into Personalized Treatments

Explore broad trends in disease and highly specific similarities in patients to craft effective, patient-specific treatment plans.

Enable Collaborative Treatment

Easily share data across networks, bringing the finest minds and broadest experiences together for the best treatment of every patient.

Register with LabKey

Download LabKey Server

Install LabKey Server

Begin Using LabKey Server

Here are some ways to get started using LabKey Server:

Other Installation Options

For additional information, troubleshooting help, and other installation options, see Install LabKey.

Feature Highlights of Version 17.1

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

Community News

Visualizations

• Time Charts - Time charts have been incorporated into common chart designer. (docs)
• Plotting Numeric Values in Text Columns - The server can now create plots for text columns that contain numbers. Non-numeric values such as '<1' representing values below or above the limits of quantitation will be ignored, allowing users to create visualizations from columns that contain a mix of numeric and text values. (docs)
• Bar Chart Enhancements - Incorporate data from more columns using bar groupings. (docs)
• Column Statistics -- New statistics include Median, Median Absolute Deviation, Quartiles, and Interquartile Range. Simplified UI for all column summary statistics. Available in LabKey Server Premium Editions. (docs)
• Grid Export - Specify how column headers are exported with data grids. (docs)

Instrument Data

• Assay Request Module - An extension of the Issues module designed especially for the assaying of samples/specimens. Available in LabKey Server Premium Editions. (docs)
• (NAb) Quality Control - Exclusion and comments for NAb assay data. (docs)
• (NAb) Statistics - Display %CV (percent coefficient of variation) on NAb assay result graphs. (docs)
• (Luminex) Quality Control - Exclude analytes from singlepoint unknown samples. (docs)
• (Genotyping) MiSeq - Support for new FASTQ header formatting. (docs)
• (Proteomics) Panorama Statistics and Quality Control
• Moving Range, Mean Cumulative Sum (CUSUMm), and Variability CUSUM plots to Levey-Jennings plots in Panorama QC folders. (docs)
• Summary hover tooltips show statistics for all methods. (docs)
• Pareto plots include data from mR and CUSUM for all guide sets. (docs)
• QC Plot interface enhanced with size/layout flexibility, legend options, etc. (docs)
• QC folders automatically delete previously uploaded Skyline documents that are redundant with new imports. (docs)

Sample Sets

• Sample Ids - New flexible options for naming samples in sample sets. Build a unique id for each sample using fields from the current row, random numbers, iterating integers, etc. (docs)

Study

• Delete Multiple Visits - Improved study management by deleting multiple visits or timepoints in a study. (docs)
• Cancel Import - Elect to stop import of a study if it would create new visits for imported data. (docs)
• Disallow Visit Overlap - Import of a visit map will fail if there are visits with overlapping time periods. (docs)
• Thumbnail Image Deletion - The user interface now provides for a way to delete custom icons and thumbnail images. (docs)

Administration

• FISMA Compliance Enhancements - Available in LabKey Server Premium Editions.
• Configure user accounts to expire after a set date. (docs)
• Disable user accounts after periods of non-use. (docs)
• Notify administrators if audit logging fails. (docs)
• Limit the allowable number of login attempts. (docs)
• Restrict identity service providers to only FICAM approved providers. (docs)
• On Server Folder Copy - Populate a new folder from an existing folder on the server without first exporting to an archive. (docs)
• New Role - Message Board Contributor This new roll allows participation in message board conversations. (docs)
• Disable Discussion Link - Ability to disable object-level discussions at the site or project level. (docs)
• Pipeline enhancements - Manage multiple pipeline protocols in a new web part. (docs)

NLP and Document Abstraction

• Improved Document Queuing - An improved task list allows the user to control the sequence of documents they process and makes it easier to reopen processing if they mistakenly approve a document. (docs)
• Case Status API - Obtain the calculated case status value via API. (docs)
• Document Batching - Abstractors can manage their task list by 'batching' related documents.

Adjudication

• Improved Upload Interface - Clearer upload interface clarifying what will happen and which steps are optional. (docs)
• Case Data Updates - New case data can be added even after a determination has been reached. New data can replace or be merged with existing case data. (docs)
• Infection Monitor Interface. Infection monitors are no longer notified unless an infection is confirmed. (docs)

Documentation

• Workflow Tutorial - Shows how to set up a new business process workflow on LabKey Server.
• Tutorial: Electronic Lab Notebook - Shows how to set up a simple sample and experiment tracking application using basic LabKey Server user interface components.
• Sample Sets: Examples - Improved sample set examples show how to provide unique sample ids, track parentage/lineage, and more.
• LabKey User Conference Resources - User presentations and slide decks from previous LabKey User Conferences.
• Query Metadata: Examples - Improved examples show how to use query metadata to modify data grids.
• Assay Feature Matrix: Reference page for features included with assay types.
• Electronic Health Records (EHR): Expanded documentation of electronic health record (EHR) features and extensibility.

Development

• Gradle Build Framework - LabKey Server developers can now build the server from source using the Gradle build framework. Ant build targets will be removed in release 17.2. (docs)

Operations

• MS SQL Server Installation
• Improved installation of PremiumStats CLR functions when required. (docs)
• Improved installation of GROUP_CONCAT script when required. (docs)

Upcoming Features

Some features we are currently working on for the 16.3 release of LabKey Server:

• Release Notes 17.2
• What's New in 17.2
• Documentation: New Workflow Tutorial

Recent Documentation Updates

Click the links below to see the most recent changes to the LabKey Server documentation.

These tutorials provide an "hands on" introduction to the core features of LabKey Server, giving step-by-step instructions for building solutions to common problems.

They are listed roughly from simple to more complex. You can start with the New User tutorials, or you can start with a tutorial further down the list that interests you.

Feature Demonstrations and Hands-On Experiences
Overview of LabKey Server:		Try a few features now in our hands-on grid demo:
Visualizations made easy with the Plot Editor:		Learn to navigate LabKey projects and folders:
Take a click-through tour of a LabKey Study:		Introducing LabKey Biologics:

Related Topics

• More Videos and Demos
• User Presentations
• Upcoming Webinars

What is LabKey Server?

LabKey Server provides data-related solutions for clinical, laboratory, and biotech researchers. Feature highlights include: research collaboration for geographically separated teams, open data publishing, data security and compliance, as well as solutions for complex data integration, workflow, and analysis problems. LabKey Server is a software platform: a toolkit for crafting your own data and workflow solutions. It is highly flexible and can be adapted to many different research and laboratory environments. You can keep your existing workflows and systems using LabKey Server to augment them, or you can use LabKey Server as an end-to-end workflow solution.

Who uses LabKey Server?

Academic researchers, clinicians, and biotechnical professionals all use LabKey Server to support their work. LabKey Server provides a broad range of solutions for data collaboration and security, clinical trial management, data integration and analysis, and more. Please visit LabKey.com to learn more.

Which assay instruments and file types does LabKey Server support?

LabKey Server supports all common tabular file types: Excel formats (XLS, XLSX), Comma Separated Values (CSV), Tab Separated Values (TSV). LabKey Server also recognizes many instrument-specific data files and metadata files, such as Flow Cytometry FCS files, ELISpot formatted XLS files, and many more. In general, if your instrument provides tabular data, then the data can be imported using a "general purpose" assay type. You may also be able to take advantage of other specific assay types, which are designed to make the most of your data. For details, see the documentation for your instrument class. Both general and instrument-specific assay types are highly-flexible and configurable by the user, so you can extend the reach of any available type to fit your needs. Contact LabKey if you have problems importing your data or have specific questions about which file types and instruments are supported.

When will the next version be released?

New features are released three times a year. Release dates can be found in our release schedule.

Who builds LabKey Server?

LabKey Server is designed by the researchers who use it, working in collaboration with LabKey's professional software developers.

How much does it cost?

All source code distributed with the Community Edition is free. Third-parties can provide binary distributions with or without modifications under any terms that are consistent with the Apache License. LabKey provides Community Edition binary distributions for free. Premium Editions of LabKey Server are paid subscriptions that provide additional functionality to help teams optimize workflows, securely manage complex projects and explore multi-dimensional data. These Premium Editions also include LabKey’s professional support services and allow our experts to engage with your team as long-term partners committed to the success of your informatics solutions.

What equipment do I need to run LabKey Server?

LabKey acts as a web server and relies on a relational database server. It can be installed and run on a stand-alone PC, or it can be deployed in a networked server environment. You can deploy the server within your organization's network, or we can deploy and manage a hosted solution for you. Single laboratory installations can be run on a single dedicated computer, but groups with more computationally demanding workflows routinely integrate with a variety of external computing resources.

Who owns the software?

LabKey Server Community Edition is licensed under Apache License 2.0, with premium features licensed under a separate LabKey license. Developers who contribute source code to the project make a choice to either maintain ownership of their code (signified via copyright notice in the source code files) or assign copyright to LabKey Corporation. Source code contributors grant a perpetual transferable license to their work to the community under terms of the Apache License. The Apache License is a broadly used, commerce-friendly open source license that provides maximum flexibility to consumers and contributors alike. In particular, anyone may modify Apache-licensed code and redistribute or resell the resulting work without being required to release your modifications as open source.

Do I need to cite LabKey Server?

If you use LabKey Server for your work, we request that you cite LabKey Server in relevant papers.

How can I get involved?

There are many ways to get involved with the project. Researchers can download and evaluate the software. You can join community forums for Proteomics, Flow Cytometry, and Study. Java Developers can enlist in the project, set up the build environment, and join the Developers Center. Research networks, laboratories, foundations, and government funding agencies can sponsor future development. Software vendors can develop proprietary modules. Developers interested in building from source or creating new modules should visit the Developer Center.

How can I find documentation for older versions of LabKey Server?

See the links below for release notes from previous versions and archived documentation:

• Release Notes Archive
• Documentation Archive

Do you have a press contact?

For media and conference inquiries about LabKey Server, please contact:

Kelsey Gibson
kelseyg@labkey.com

How to Cite LabKey Server

If you use LabKey Server for your research, please reference the platform using one of the following:

General Use: Nelson EK, Piehler B, Eckels J, Rauch A, Bellew M, Hussey P, Ramsay S, Nathe C, Lum K, Krouse K, Stearns D, Connolly B, Skillman T, Igra M. LabKey Server: An open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 2011 Mar 9; 12(1): 71.

Proteomics: Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whitaker J, States D, Hanash S, Paulovich A, McIntosh MW: Computational Proteomics Analysis System (CPAS):  An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments. Journal of Proteome Research 2006, 5:112-121.

Flow: Shulman N, Bellew M, Snelling G, Carter D, Huang Y, Li H, Self SG, McElrath MJ, De Rosa SC: Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials. Cytometry 2008, 73A:847-856.

Additional Publications

A full list of LabKey publications is available here.

Documentation Archive

This section contains an archive of the "What's New" and "Release Notes" for specific versions of LabKey Server.

• Documentation Archive.
• Previous Releases - list of all previous releases along with release date, download links, and source control revision number.

Release Notes Archive

Feature Highlights of v16.3

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

Community News

Visualization

• Bar and Pie Charts - Two new built-in visualization types are now available: Bar Charts and Pie Charts. (video)
• Chart Designer: A new chart designer is available for a wide range of built-in visualization types, featuring drag-and-drop column selection and a more intuitive layout of configuration options. (docs) (video)
• Improved Data Views: A new setting lets you control the display height for the Data Views web part. (docs)
• Binning for Large Data Sets: Data point binning improves the readability of scatter plots over large data sets. (docs)
• (Premium Editions) Additional Column Summary Statistics: New statistics options have been added, including standard deviation and standard error. (docs) (video)

System Integration

• R Studio Integration: Design R reports in RStudio using data selected in LabKey Server. Contact LabKey for set up and support options.
• New SQL Methods: The SQL methods GREATEST and LEAST are now supported for PostgreSQL, MS SQL Server, Oracle, and MySQL. (docs)
• ETL Engine Improvements
• Improved PostgreSQL Scalability: A limitation has been removed that imposed a limit of 100 columns on PostgreSQL tables that are targets of an ETL process.
• Alternate Key: Use an alternate key, instead of the target table's primary key, when merging data with an ETL process. (docs)
• Set Range: Developers can use ranges to aid development of ETL scripts. (docs)
• Transformation Improvements: ETL transformation using a Java class is now supported. (docs) ETL processes may now output constant values into a target column. (docs)

Security

• Improved Duo Configuration: A new option lets you indicate how LabKey Server user accounts are matched to Duo accounts, either by user id, user name, or email address. (docs)

Administration

• Date and DateTime Data Types: Date and DateTime data types are more intuitive to use. Admins can set default formats for each type at various scopes in the server. (docs)
• Apply a Template to Multiple Folders: When importing a folder archive, you have the option to select a subset of objects to import, and can also choose to apply that template to multiple folders simultaneously. (docs) (video)

Study Data Management

• New UI for Assay Schedule: The process for scheduling assays has been simplified. (docs)
• New UI for Vaccine Study Products and Treatments: Simplify study registration and making immunization products consistent and manageable across multiple studies. (docs and docs)
• Study Performance Improvements: The underlying database schema for studies has been redesigned, providing greater performance and using less storage space in the database.

NLP and Document Abstraction

• Natural Language Processing: Use the LabKey NLP engine or integrate another to extract data from free text documents and reports. (docs)
• Document Abstraction Workflow: Improved document abstraction workflow, including options for manual abstraction, automatic abstraction, and document review. (docs)
• Disease-based Document Assignment: Specialize abstraction workflow and assignments based on the disease group represented in the document. (docs)
• Document Abstraction UI: More intuitive interface streamlines the process of abstracting information from documents. (docs)

Assays / Instrument Data

• Signal Data Module: Capture data and metadata for HPLC experiments. (docs)
• Sample Sets: Samples in different containers can be resolved in a single sample set. (docs) (video)
• (Luminex) Retain Exclusions when Reimporting Runs: If you have excluded wells, analytes, or titrations, you can opt to continue excluding them on reimport. (docs) (video)
• (Luminex) Ignore Bead Numbers on Analytes: Bead numbers are no longer included as part of the analyte name. (docs)
• (Panorama) Performance Improvements: The internal queries used by Panorama have been optimized to improve page load times.

Development

• Improved Study Export/Import: The dataset_metadata.xml file in a study archive now provides: (1) an <index> tag to indicate index fields, (2) a <sharedConfig> tag to indicate columns that should be added to all the datasets, and (3) on import of a study archive, the <scale> tag (which holds column size information) is applied to existing columns in the target study. (docs)
• API Session Key: Run client API code in the context of a user account without storing your credentials on the client machine. (docs)

Operations

• New supported versions:
• PostgreSQL 9.6 (docs)
• SQL Server 2016 (docs)
• Apache Tomcat 8.5.x: version 8.5.9 and later only (docs)

Potential Backwards Compatibility Issues

• Support for PostgreSQL 9.1 has been removed.

Upgrade to 16.3

• Upgrading the Issues Module. If the server is restarted prematurely during upgrade, the issues tracker migration code will not be re-run automatically (because it is implemented as a deferred upgrade script). To run the upgrade code manually go to this URL: ./labkey/issues/home/upgradeIssues.view It will trigger the same upgrade code that the automatic upgrade should have run. For more details see Support Ticket #27963.

Documentation

• LabKey User Conference 2016 Resources: (docs)

Feature Highlights of v16.2

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

LabKey User Conference 2016 Speakers Announced

Join us for the 2016 LabKey User Conference & Workshop! At this two day event, attendees will have the opportunity to:

• Hear how leading users are improving efficiency, transparency, and data quality with LabKey Server
• Enhance their technical knowledge of the LabKey Server platform
• Receive hands-on technical guidance from LabKey developers
• Learn the fundamentals of LabKey Server administration and core capabilities of the platform
• Connect and collaborate with other LabKey Server users

Dates: October 6 – 7
Location: Seattle, WA
Venue: Pan Pacific Hotel, 2125 Terry Avenue, Seattle, WA 98121

Learn More and Register: http://www.labkey.com/about/events/2016-user-conference/

LabKey Biologics Preview

Collaboration

• Improved Issue Administration: The Issues administration page has been re-organized for clarity. The custom field editor has been updated to use the standard field editor. The number of custom fields that can be added is now unlimited. Multiple issue lists in the same container are supported. Individual issues can be moved between containers. Inheriting configuration from another issues list is no longer supported, but custom fields can be set as lookups to shared lists via the standard field editor. (docs) (demo)

Study Data Management

• FreezerPro Enhancements: Add custom fields via the field mapping user interface. To ensure appropriate field mapping, the user interface now filters by data type. Refine data loaded from the FreezerPro server with expanded filter comparators. (docs) (demo)

Administration

• User Account Improvements: Users can update their own email address. (docs) (demo)
• Data Views Performance Improvements: The Data Views Browser loads faster, making it easier for users to explore the queries and reports in a study.
• Improved Query Browser Performance: The Query Browser loads faster, making it easier for administrators to browse the core database tables and the queries built on top of them.

Visualization

• Column Visualizations: Small charts for one column of data, including Histograms, Box Plots, and Pie Charts. (docs) (demo)
• Column Aggregates: Display aggregate values at the bottom of a data column, including Average, Count, etc. (docs) (demo)
• Quickly Remove Column: Quickly remove a column from a data grid through the column header menu. (docs) (demo)
• Improved Menu Layout for Data Grids: The "Views" menu has been renamed to "Grid Views", and focuses exclusively on modifying grids. The new "Reports" menu consolidates the available report types. (docs) (demo)
• R Markdown v2: Markdown v2 is now supported when creating knitr R reports. (docs)

User Interface

• User Interface Tours: Shows users how your application works by providing a step by step path through the UI, each step provides a pointer, explanatory text, and links to the next step and further documentation. (docs)
• New Icons: Most of the user interface has been updated from bitmap icons to use font-based icons. Views (docs)
• Reorder Reports and Charts: Administrators can reorganize reports within categories. (docs) (demo)
• Reorder Subcategories in Data Views Browser: Administrators can reorder subcategory groupings using a drag-and-drop interface.(docs) (demo)
• Alphabetize Items in Data Views Browser: Administrators can order items alphabetically or according to the order they are returned from the database. (docs) (demo)
• Notifications Inbox: An experimental feature displays a notification inbox in the upper right corner. (docs) (demo)

Sample Sets and Specimens

• New Data Structure: DataClass: Use DataClasses to capture properties and parentage for samples, such as those produced from complex bio-engineering processes. (Also available in release 16.1.) (docs)
• Sample Parentage/Lineage: A new way to indicate parentage in Sample Sets has been added. The previous way to indicate lineage, the "Parents" column, is still present, but should be considered deprecated. (docs)

Security

• SAML Authentication: SAML authentication is now supported. Available in LabKey Server Professional, Professional Plus, and Enterprise Editions. (docs) (demo)

Assays and Instrument Data

• (Panorama) QC Dashboard Improvements: The Quality Control Dashboard shows a summary of the most recent file uploads, along with color-coded QC reports. (docs) (demo)
• (Panorama) Small Molecule QC: Panorama QC folders now support both proteomics (peptide/protein) and small molecule data. (docs) (demo)
• (Panorama) Heat Maps with Clustergrammer: Visualize expression matrix data using the Clustergrammer web service. (docs)
• (MS2) Multiple FASTAs for Single Search: XTandem and Mascot searches can be performed against multiple FASTAs simultaneously. (docs) (demo)
• (MS2/Mascot) Improvements in Mascot Search Results: Propagate the FDR filter applied to the decoy results to the target peptide results. (docs) (demo)

Documentation

• Improved List Tutorial: Learn about using lists. (docs)
• Tours for New Users: Create tours of tools and interfaces for your users. (docs)
• Improved Examples for Surveys: Additional example code for online surveys is provided, including populating default values from database values, conditional/branching questions, and Likert scales. (docs)

Development

• Rlabkey Source Repository: The Rlabkey API has been moved from SVN to GitHub.

Feature Highlights of v16.1

• FreezerPro - A new user interface makes it easy to connect to and import data from your FreezerPro installation.
• Panorama Enhancements - Analyze small molecule data, and track performance metrics on an improved quality control dashboard.
• User Interface Features - Preview file contents and images; customize message board notifications; upgrade without administrator login.

Community News

LabKey User Conference 2016: Save-the-Date

Mark your calendar for the LabKey User Conference 2016! This year’s LKUC will take place October 6-7 in Seattle, WA. Stay tuned for additional details and registration information.

Zika Real-Time Data Sharing

LabKey partners at the O’Connor Lab at University of Wisconsin Madison have been making headlines with their real-time sharing of Zika research data via LabKey Server. Dave O’Connor and his colleagues are sharing raw-data, study commentary, and results with the public, updating available information daily. To see the live Zika data, visit the O’Connor Lab LabKey Server

Study Data Management

• FreezerPro: Improved setup and configuration, including a graphical user interface for selecting specimen types and mapping columns. Improved performance when importing data. Available in LabKey Server Professional, Professional Plus, and Enterprise Editions. (docs)
• Adjudication Module: Facilitate independent assessments of a given case, where two or more assessors have access to the same data, but none can see any other's decision before they have made their own determination. Used for gaining confidence that a given diagnosis or decision is correct. (docs)

Assays / Instrument Data

• (Panorama) Quality Control Dashboard: Quality control summary is based on data in subfolders. New metric added: Mass Accuracy. Graph both precursor and fragment values on the same plot. (docs)
• (Panorama) Small Molecule Support: Support for storing and viewing small molecule data via Skyline documents. (docs)
• (Panorama) Automatically Link Skyline Document Versions: When importing Skyline documents, different versions of the same document are automatically linked together. (docs)
• (Mass Spec) Configure Mascot at the Project or Folder-level: Use the site-wide Mascot configuration as the default; use the project and folder-level configuration to override the site-wide configuration. (docs)
• (Mass Spec) Mascot-specific Details: Additional details are now imported from Mascot search results, including metadata, decoy, and alternative peptide information. (docs)
• (HPLC) HPLC Assay Design: A new HPLC module includes an HPLC assay design, supports automatic or manual upload of result files, and contains overlayed chromatogram visualizations for multiple runs. (docs)

User Interface

• Hover for File Preview: Hover over a file icon in the repository to see a preview of the file contents. (docs)
• Display Image Thumbnails in a Grid: Display inline thumbnails for file and attachment fields in lists, sample sets, or assay result grids. (docs)
• Customizable Email Templates for Announcements: Customize the email sent for message board activity. (docs)

Security

• Security Bulk Update API: Supports programmatic update of security groups and role assignments. Improved import of groups from external systems. (docs)

Development

• Trigger Scripts: Trigger scripts can now be applied when importing data to Lists. (docs) | (docs)
• Transform Scripts: Assay import using transformation scripts now can include warning reporting, offering the user the option to proceed or cancel the import. (docs)
• Long Text Strings: For administrator defined tables such as lists, datasets, and assay results, text columns can now hold the maximum number of characters allowed by the underlying database implementation. Previously, LabKey Server limited string columns in these tables to a maximum of 4000 characters, regardless of the maximum length allowed by the database implementation. (docs)

Operations

• Improved Server Upgrade Process: Starting in 16.1, the server initiates upgrade and startup of all modules at server startup time. Administrators can still log in to view upgrade/startup progress, but the server will no longer wait for a login. Previously, the server would upgrade the core module at server startup, but would wait for an administrator login before upgrading other modules or initiating module startup. This change streamlines the startup process, simplifies upgrade code, and facilitates scripted upgrades of LabKey Server.
• Support PostgreSQL 9.5: For details, see Supported Technologies.
• New Full-Text Search Administration Option: A new option lets you specify the directory type used by the underlying full-text search library. In most cases, we recommend using the default setting. If you encounter problems with full-text search, contact LabKey for recommended changes to this setting. (docs)

Potential Backwards Compatibility Issues

• Default Request URL Pattern Change: New default URL pattern, for details see LabKey URLs.

Feature Highlights of v15.3

• Custom Footers and Login Pages - Tailor your site with custom footers and login pages.
• SQL Query Logging - Query logger tracks who has queried the database, when, and what SQL query was used.
• Document Revision Tracking - Refine mass spectrometry method development with document version tracking.
• ETL Column Mapping - Copy data between tables with different column names with ETL column name mapping.

Community News

• User Conference Videos and Slide Decks - Presentations from the 2015 user conference are now available as videos and slide decks.
• Genomics England - Genomics England is partnering with LabKey to design and develop a solution that will integrate and securely share complex clinical and genomic data for the 100,000 Genomes Project.
• Just Biotherapeutics - Just Biotherapeutics, Inc. and LabKey are teaming up to develop a new software product that help will biotechnology R&D teams produce more effective and affordable biotherapeutics by optimizing the development process.
• Premium Editions - LabKey Software has introduced Premium Editions of LabKey Server. For feature details of each edition, see LabKey Server Editions.

Extract-Transform-Load (ETLs)

• Undo ETL job: Roll back changed records in the target table. (docs)
• Column name mapping: Copy data between tables, even when their columns names do not match. (docs)
• Call an ETL job from another ETL job: ETLs can queue up other ETLs, even ones that exist in a different module. (docs)
• Stored procedures as gates for ETLs: Let a stored procedure determine if there is work for an ETL. (docs)
• ETL job history table: View a history of all ETLs that have run on the site. (docs)

Look and Feel

• Turn off default LabKey footer: Remove the default LabKey Server footer. Available in LabKey Server Professional, Professional Plus, and Enterprise Editions. (docs)
• Custom footers: Add a custom footer to replace the default LabKey Server footer. (docs)
• Custom login page: Provide a custom login page that replaces the default login page. (docs)

Security

• User self-registration: Administrators can let users create their own accounts on the server. (docs)
• Automatic user registration: Administrators can enable or disable auto-creation of new accounts in LDAP and SSO authentication systems. (docs)
• SQL query logging: Log each query request against an external data source including the user, impersonation information, date and time, and the SQL statement used to query the data source. Useful in applications that require review of data retrievals. Available in LabKey Server Professional Plus and Enterprise Editions. (docs)

Assays / Instrument Data

• (MS2) Merge XTandem search results: Combine existing XTandem search results into a merged analysis. (docs)
• (Panorama Mass Spec) Document revision tracking: Keep track of refinements to mass spec methods by linking different versions of a document into a series. (docs)
• (Panorama Mass Spec) Pareto plots: Pareto plots provide a summary of outlier values, identifying the most likely causes of quality control problems. (docs)
• (NAb) Improved handling of NAb data: On import, NAb dilution and well data is now stored in the database in two new tables, DilutionData and WellData, instead of being stored as a file on the server. Users can write queries against, and export from, these new tables. Also, the run details view is rendered from the new tables, instead of being parsed from the original data file. Note that on upgrade to LabKey Server 15.3, existing NAb data files on the server will be parsed and imported to the new database tables. (docs)
• (Genomics) PacBio support: Manage samples and sequencing results generated from a PacBio Sequencer. (docs)

Data Integration

• Improved schema export: The schema export dialog now lets you provide a target schema and a target directory for the exported files. (docs)

Operations

• Support for Tomcat 8: (docs)
• Performance: Improved caching performance for queries and custom views.

Development

• (Python) Export data as a python client script: Support Python clients of LabKey Server by generating a Python script that retrieves data from the database. (docs)
• (Python) Assay data support: New methods in the Python Client API support assay data (loadBatch and saveBatch). (docs)
• (Python) Support for Python 3: The updated Python Client API supports Python 3. (docs)
• Site validation enhancements: New site validation checks show (1) folders where Guests have read permissions and (2) pipeline roots that don't exist in the file system. (docs)

Potential Backwards Compatibility Issues

• Microsoft SQL Server: Starting in LabKey Server 15.3, Microsoft SQL Server 2008 R2 is no longer supported.
• Java 7: Starting in LabKey Server 15.3, Java 7 is no longer supported.

Highlights of v15.2

• Analyze - Explore plate results for FluoroSpot, a multi-cytokine variant of ELISPOT
• Integrate - Join Gene Ontology annotations with expression data
• Share - Support compliant data sharing with site-wide terms of use
• Monitor - Visualize quality control ranges using guide sets in Panorama
• Migrate - Transfer schemas and security groups, users and roles

LabKey User Conference

Registration is open for the LabKey User Conference and Workshop 2015, October 1 and 2 in Seattle. Seats sold out early last year, so register soon. Hope to see you there!

Community News

• HICOR: The Hutch Institute for Cancer Outcomes Research (HICOR) debuted the HICOR IQ portal, enabling HICOR partners to visualize cancer incidence, survival and insurance claims data to help them improve care. Covered in the Hutch News.
• O'Connor Lab: A new case study describes how Professor David O’Connor’s lab at the University of Wisconsin uses LabKey Server as its “operating system,” speeding its efforts to understand how genetics affects immunity.
• Natural Language Processing (NLP): The Fred Hutch and LabKey are collaborating to develop tools for NLP-assisted clinical data abstraction and annotation workflows, as covered in the Hutch News.
• Argos: Also as reported in the Hutch News, the Argos data exploration technology is now in pilot use at the Fred Hutch, helping teams perform hypothesis generation, trial accrual estimation and cohort discovery in a HIPAA-compliant manner.

Assays / Instrument Data

• FluoroSpot Assay: New assay type to support FluoroSpot experimental results. Results can be viewed in a graphical representation of the experimental plate, with selectable highlights for given samples and antigens. (docs)

• Protein Expression Matrix Assay: New assay type to support protein expression matrix results. (docs)
  === Sponsored by HIRN - Human Islet Research Network

• GO (Gene Ontology) Annotation Improvements: Imported GO annotations are now queriable, making it possible to include them in custom SQL queries, reports, and charts, and to join them with related data, such as protein expression and mass spectrometry data. (docs)
  === Sponsored by HIRN - Human Islet Research Network

• (Mass Spec) Guide Set for Panorama Quality Control Plots: Visualize the expected range of values in the quality control dashboard. (docs)
  === Sponsored by Panorama Partners Program members

Data Integration / Studies

• Auto Generation of Schema Export Scripts: Auto-generate a migration script for moving tables and data to a different environment/schema. (docs)

• (Experimental Feature) Shared Demographic Datasets and Timepoints: Use a common set of participant and visit data in multiple studies simultaneously. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

Collaboration

• Site-wide Terms of Use: Require users to agree to a 'terms of use' when logging into the site. The terms of use is scoped to the entire site as a whole, instead of scoped to an individual project. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Folder Display Title: Display titles can be specified for folders that can be different from the underlying folder name. (docs)

• File Upload for Sample Sets: Upload new sample sets from a file. Supported formats include: tab-separated value files (TSV) or Excel files (XLS and XLSX). (docs)

Security

• Export/Import Permission Settings: Propagate security configurations from one environment to another. (docs)
  === Sponsored by Fred Hutchinson Cancer Research Center

• Single Sign On Authentication: Allow users to sign on to multiple applications while providing their credentials only once to a Central Authentication Service (CAS) Server. (docs)
  === Sponsored by University of South Florida Health Informatics Institute

Extract-Transform-Load (ETLs)

• ETL Auto Restart: ETL jobs requeue and restart if the server shuts down during the job.
  ===Sponsored by SNPRC - Southwest National Primate Research Center

Development

• Module Properties: New properties for modules, including author, label, and description. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

• Generate Java Data Access Code: Export the definition of any data grid as Java code. Use this code to load the data into a Java application. (docs)

Operations

• 3rd Party Software Included in the Windows Graphical Installer:
• PostgreSQL 9.4.4
• Java Runtime Environment (JRE) 8u45
• Apache Tomcat 7.0.62

• Site Validation Service: A new site validation service has been introduced, to help diagnose issues with schema integrity, etc. (docs)

Potential Backwards Compatibility Issues

• Java 7 no longer supported. Starting with version 15.2, LabKey Server no longer supports Java 7. Please upgrade to Java 8. (docs)

• PostgreSQL 9.0.x no longer supported. We recommend upgrading to the latest point release of PostgreSQL 9.4.x. (docs)

• Email Notification for Specimen Requests. After upgrading to 15.2, existing studies may need to have their specimen email notifications reconfigured. To do this, go the study in question, click the Manage tab and click Manage Notifications (near the bottom of the page). Inside the text boxes Notify of New Requests and Always CC, hit the Enter key in between each email entry. Failing to reconfigure the notifications in this way may result in notifications being sent to only the first email address in each list.

• Email Unregistered Addresses: In LABKEY.Message, the parameter 'allowUnregisteredUser' (which allowed logged-in users to send emails to unregistered addresses) has been deprecated. In version 15.2, an administrator must enable email to unregistered addresses by assigning the role "Email Non-Users" to some user or group. (docs)

Highlights of v15.1

• Polish. Usability improvements, including thumbnail extraction, expanded notifications and module reload
• Quality. Nearly 500 bugs fixed, plus new QC tools for targeted mass spec and Luminex
• Performance. Speedier extract-transform-load and specimen import pipeline

Argos Debut

Argos is a LabKey-based application that helps ordinary users filter and explore clinical data and specimen resources to generate hypotheses, investigate study feasibility, and evaluate courses of treatment. Developed in partnership with the Fred Hutchinson Cancer Research Center, the first version of Argos relies upon the Caisis data model, so early adoption is easiest for those with existing Caisis installations. To explore Argos, see the 6-minute video and Fred Hutch overview. For further details, please contact LabKey.

Community News

• ITN TrialShare: As reported in the New England Journal of Medicine, participant-level results from the Immune Tolerance Network's groundbreaking study on prevention of peanut allergies are now publicly available on the ITN's award-winning TrialShare clinical research portal.
• Panorama: New tools for reviewing assay performance trends for targeted mass spec data will be covered at the American Society for Mass Spectrometry (ASMS) Conference this spring. Look for the June 2 poster and March 31 user group meeting.
• Primate EHRs: A new case study explores the electronic health record (EHR) system developed in partnership with the Oregon and Wisconsin National Primate Research Centers (ONPRC & WNPRC), which will soon be used by the Southwest National Primate Research Center (SNPRC).
• Adair/Kiem Labs: Another new case study explores how the labs of Jennifer Adair and Hans-Peter Kiem at the Fred Hutch use LabKey Server to speed efforts in development of stem cell gene therapy for wide range of diseases, from HIV/AIDS to cancers.

Studies

• Dataset tagging: A new tag property added to datasets lets you group datasets by keyword. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Republish study: Republish a previously published study using the same settings. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Expanded notification options: Receive notifications for all changes to reports and datasets, or changes in particular categories. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Extraction of thumbnail images: Thumbnail images embedded in Word, Excel, and PowerPoint documents can be automatically integrated into data views. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Improved time charts: Time charts now handle large numbers of participants. User interface for time charts offers pagination for large numbers of participants.
  === Sponsored by University of South Florida Health Informatics Institute

Specimens

• Specimen importer: Performance for the specimen importer pipeline has been improved. (video)
  === Sponsored by HVTN - HIV Vaccine Trials Network and ITN - Immune Tolerance Network

Collaboration

• Data pipeline: When you process and upload data, the data pipeline remembers and returns to the last directory you visited. (docs)

• Auto-completion: Username and email fields have improved auto-completion in the following areas: specimen requests, issues, messages, and user/permissions management.

• Issues management: Issue lists can inherit admin settings from another folder, simplifying and consolidating administration tasks when managing multiple issues lists. (docs)

• Full-text search: Improved performance for full-text search.
  === Sponsored by O'Connor Labs, University of Wisconsin

• ETL (Extract-Transform-Load) improvements - (video)
• Performance has been improved for large jobs.
• Support for cancellation of running jobs. (docs)
• Support ETLs into target tables which have JavaScript Triggers Scripts.
• A bulkLoad option minimizes logging and processing overhead. (docs)
• Allow finer granularity of transaction size when writing into the target table, including no transaction option. (docs)
  ===Sponsored by SNPRC - Southwest National Primate Research Center
• ETL export to files, such as TSV and CSV files. (docs)
• Support for pipeline command tasks in ETLs. (docs)
• Support for stored procedures which return result sets; use the result set as source query. (docs)
• Support for stored procedures that pass parameter values to further stored procedure steps in the same ETL. (docs)
  === Sponsored by Fred Hutchinson Cancer Research Center

Assays / Instrumental Data

• (ELISpot) Handle "too numerous to count" values: Instrument codes for "too numerous to count" are recognized and excluded from calculations. (docs)

• (Luminex) Improved quality control reports: Quickly view the Levey-Jennings plots directly from the QC report page. (docs)
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

• (Luminex) Guide sets: New user interface lets you manage and delete guides sets. (docs)
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

• (Luminex) Disable flagging: When a metric has too few runs to be useful as a quality control guide set, you can selectively disable flagging for that metric. (docs)
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

• (Luminex) Run re-calculations as a pipeline job: After inspecting and choosing to exclude certain data values, the curve fit recalculation can be processed in the background using the pipeline. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• (Luminex) Levey-Jennings plots: Improved performance for calculation of Levey-Jennings plots.
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

• (NAb) Reverse dilution direction: The default direction of dilution on a plate can be reversed. (docs)
  === Sponsored by MHRP - U.S. Military HIV Research Program

• (Genotyping) Bulk update/Data cleanup: Bulk edit simplifies experiment management. (docs)
  === Sponsored by O'Connor Labs, University of Wisconsin

• (Genotyping) Feature annotations: Import feature annotation data via the script pipeline.
  === Sponsored by HIPC - Human Immunology Project Consortium

• (Panorama/Targeted Mass Spec) Quality control: Quality control folder type helps you evaluate instruments and analytes over time. (docs) (video)
  === Sponsored by Panorama Partners Program members

Development and Operations

• Recommended Java Upgrade: As part of the 15.1 release, we recommend that all users upgrade to use Java 1.8u40 or later. The end of life date for Java 1.7 is scheduled for April 2015, after which, public updates will no longer be available. (installation docs), (configuration docs)

• Module resources reload: To make development easier on a production server, many file-based module resources are dynamically reloaded (from the /deploy directory) when the server detects changes to those files.

• SQL Server synonyms: Synonyms on tables and views are supported. (docs)

• Rlabkey security: Rlabkey now defaults to TLSv1, instead of SSL3. (docs)

Potential Backwards Compatibility Issues

• Java Client API changes - HttpClient library: The underlying HTTP library used by the Java Client API has been migrated from Apache Commons HttpClient 3.1 to Apache HttpComponents HttpClient 4.3.5. We have made every effort to hide the substantial changes in the underlying library from users of our Java client API. However, some Java API methods exposed Apache classes that have been removed (e.g., HttpMethod, HttpConnectionManager, and the old HttpClient), making 100% compatibility impossible. Please test your code thoroughly against the new library. (API docs)

• Java Client API changes - Self-signed Certificates: For security reasons, the Java client API no longer connects by default with servers having self-signed certificates. Users of the API can override this behavior by calling Connection.setAcceptSelfSignedCerts(true).

• Character Encoding Changes: Study, list, and folder archives are now all written using the UTF-8 character encoding for text files, and imported archives are parsed as UTF-8. In addition, text exports from grids consistently use UTF-8 character encoding. Formerly, these operations used the server's default character encoding.

Highlights of LabKey Server v14.3

• Visualize inputs, outputs and histories for extract-transform-load (ETL) jobs.
• Explore projects and folders together through a unified interface.
• Compare categories with the bar plot API.
• Stay Informed with improved email notifications.
• Speed customization using the performance profiler and module development checklist.
• Safeguard protected health information (PHI) by logging access and intended use, as seen in HIDRA.

Resources

• LabKey Server Download
• Release Notes 14.3

User News

• Collaborative DataSpace: A new, 7-minute video shows the DataSpace vision for cross-study data exploration and cohort discovery.
• Katze Lab: The Katze team used LabKey Server for its new Science paper on Ebola susceptibility, a study featured in the New York Times.
• Hutch Integrated Data Repository Archive (HIDRA): The Fred Hutch news explored HIDRA's plans for natural language processing (NLP) of Cancer Consortium data.
• Panorama: The NCI's newly launched proteomics portal uses Panorama, the LabKey Server-based repository for targeted proteomics. A Panorama overview just went to press.

Collaboration

• Consolidated project/folder navigation menu
  This experimental feature lets you view and navigate all projects and folders on one consolidated menu. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

• PHI activity auditing
  We've added infrastructure to support auditing of user activity with PHI data. The new infrastructure provides the ability to log activity based on flexible, module-defined criteria. For example, log all SQL queries executed against a particular schema, the patient IDs involved whenever PHI data is accessed, and/or the user's stated purpose in querying the data. For more information contact us.

• Improved administration for email notifications
  The user interface for administrators has been improved, making it easier to set message and file notification behavior. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Enhanced information on report changes
  When reports are updated, we provide greater detail on the nature of the change, distinguishing between changes to a report's content (for example, the filter settings or measures displayed) and its metadata properties (for example, the report title or author). (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Improved list management
  The Manage Lists page now uses a standard grid that supports sorting, filtering, export, viewing of lists in multiple folders, and multiple select for deleting lists and exporting list archives. (docs)

Data Integration

• Extract-Transform-Load (ETL) history
  A new user interface provides detailed histories and visualizations of ETL jobs. (docs)
  ===

Visualization

• Bar plots
  A new JavaScript-based visualization type represents values as vertical bars. (docs), (examples)
  ===

Observational/Cohort Studies

• Published studies details
  A new query lets administrators view details about published and ancillary studies for a given parent study. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Study location management
  Locations associated with a study can be deleted, provided they are unused inside the study. All unused locations can also be deleted in bulk. (docs)
  === Sponsored by ITN - Immune Tolerance Network

Specimen Management

• Improved specimen views
  The fields available for rollup aggregation have been expanded to included user-added fields and vial-to-specimen rollups. (docs)
  === Sponsored by ITN - Immune Tolerance Network

Data Processing Pipeline

• Cancel running jobs
  Improved behavior for cancelling running pipeline jobs, such as specimen import/refresh jobs and published study refresh jobs. (docs)
  === Sponsored by ITN - Immune Tolerance Network

Assays/Experimental Data

• (Luminex) Negative control beads
  An improved user interface lets you select a preferred negative control bead for a given analyte. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• (Luminex) EC50/AUC controls
  You can calculate EC50/AUC for titrations without adding them to the quality control report or to Levey-Jennings plots. (docs)
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

• (Luminex) Positivity threshold importing
  LabKey Server now supports file-based import of positivity thresholds for antigens, instead of manual entry. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• (NAb) Multi-virus plate support
  The plate designer has been enhanced to support multiple viruses, controls, and specimens on a single plate. (docs)
  === Sponsored by MHRP - U.S. Military HIV Research Program

• (NAb) FileMaker metadata import
  LabKey Server now supports file-based import of metadata from FileMaker files, instead of manual data entry. (docs)
  === Sponsored by MHRP - U.S. Military HIV Research Program

• (Genotyping) Haplotype assay improvements
  The haplotype assay now supports species names and haplotype renaming. A new report shows discrepancies between STR and other haplotype assignments. (docs)
  === Sponsored by O'Connor Labs, University of Wisconsin

• (Panorama/Targeted Mass Spec) general improvements
  Support for importing Skyline file format. Improved plotting and additional plotting types. New workflow for sharing data with journals. (docs)
  === Sponsored by MacCoss Lab, University of Washington

Documentation

• Development environment setup: New checklist makes it easy to set up a development environment for simple modules. (docs)
• JavaScript Client APIs: Revised tutorial has an easier set up and code explanations. (docs)
• Module development: Revised documentation provides guidance on which sort of module to develop. (docs)
• Server API actions: New documentation explains how to develop server-based Java views, actions, and forms. (docs) | (docs)
• Luminex calculations: New documentation provides reference information on Luminex calculations. (docs)

Development

• Schema Browser: Improved performance for the Schema Browser.
• Datasets and schema: Improved performance when loading table and schema information.
• Specimen foreign keys: Improved performance for tables that have foreign keys into the specimen repository.
• Mini-Profiler: A new mini-profiler helps developers analyze code performance, such as which queries were run on a page and how much time the queries required to complete. (docs)

Potential Backwards Compatibility Issues

• Dataset import behavior change: For consistency with other data types, imported data rows are now treated as an insert (disallowing duplicates), instead of a merge. Note that this change was introduced in version 14.2.
• SQL order of precedence change: Prior to 14.3, bitwise operator precedence varied based on the underlying SQL database. We suggest always using parentheses when using bitwise operators.
• .deleted directory: After files or folders are deleted via the Files web part, they are no longer moved to the .deleted directory, instead they are directly deleted from the server. After renaming a folder, when an existing folder already has the same name, the already existing folder is moved to the .deleted directory.
• Pipeline configuration: When configuring a pipeline, LabKey Server looks for configuration files, by default, in the following directory: LABKEY_HOME/config. To reset the config directory see Configure LabKey Server to use the Enterprise Pipeline.

Highlights of LabKey Server v14.2

• Organize and share files using a new drag-and-drop file uploader (docs)
• Analyze high-volume results using Rserve to execute scripts remotely (docs)
• Integrate specimen information with automated FreezerPro® import (docs)

User News

Resources

• Download LabKey Server 14.2
• Release Notes 14.2

Collaboration

• Native, browser-based drag-and-drop file uploader. New uploader works out of the box, requiring no Java applets to install or configure. (docs)

• Improved pipeline processing for scripts and external commands. Supported scripts include R, Python, Perl, and others. Set output directories and file names. Job deletion can delete associated experiment runs. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

• Rserve integration. Generate R reports on a remote Rserve server. (docs)
  === Sponsored by Fred Hutchinson Cancer Research Center and HIPC - Human Immunology Project Consortium

• Export selected records. Export individual or multiple records that have been selected in a data grid. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• Between/not between filters. Filter by value range. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

• Improved Data Views web part. Authors and editors can edit/delete reports in the Data Views panel/web part. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium

• Email notifications. Receive notification when the content of a report or dataset changes. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Improved user interface and documentation for impersonating users, groups, and roles. (docs)

Observational Studies

• Improved import/export of shared study data and metadata. (docs)
  === Sponsored by CAVD - The Collaboration for AIDS Vaccine Discovery via the Bill and Melinda Gates Foundation

• Faster performance for study archive export & import.
  === Sponsored by ITN - Immune Tolerance Network

• Import and export custom study properties in study archives. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Manage study products. Define and share vaccine treatment protocols and schedules across studies. (docs)
  === Sponsored by CAVD - The Collaboration for AIDS Vaccine Discovery via the Bill and Melinda Gates Foundation

Specimen Management

• Customizable specimen report webpart, allowing display of reports by participant, cohort type, requested by location, and others. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Improved FreezerPro integration. Import data directly into the specimen management system on demand or on a regular schedule. (docs)
  === Sponsored by a major pharmaceutical corporation.

• Improved export and import of specimen repository settings. (docs)
  === Sponsored by ITN - Immune Tolerance Network

• Improved specimen refresh. In published studies, update the user that performs the specimen refresh. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• New specimen rollup rules for Combine and LatestNonBlank. (docs)
  === Sponsored by HVTN - HIV Vaccine Trials Network

• Faster performance for specimen archive import.
  === Sponsored by HVTN - HIV Vaccine Trials Network

Assays

• (Luminex) Use historical means for Levey-Jennings plots. (docs)
  === Sponsored by CAVD - The Collaboration for AIDS Vaccine Discovery via the Bill and Melinda Gates Foundation

• (Luminex) Skip Ruminex calculations. (docs)
  === Sponsored by CAVD - The Collaboration for AIDS Vaccine Discovery via the Bill and Melinda Gates Foundation

• (Haplotype) Improved Haplotype assay. New report types, add data for additional species. (docs)
  === Sponsored by University of Wisconsin - O'Connor Lab

• Participant/visit resolvers. Use an existing list from another source. Set default values. Simplify upload and improve consistency. (docs)
  === Sponsored by CAVD - The Collaboration for AIDS Vaccine Discovery via the Bill and Melinda Gates Foundation

• Reduce assay user input error. Guidance for using defaults and validation. (docs)

Documentation

• Context sensitive help. New context-sensitive help links navigate directly to the relevant documentation topic. (docs)
• Project/Folders Best Practices. New documentation provides dos and don'ts for setting up projects and folders. (docs)
• Guidance for preparing data for import into LabKey Server. (docs)
• Updated documentation for using saved filters and sorts. (docs)
• Updated File Repository Tutorial. New step provides an advanced keyword and search application.
• Updated Collaboration Tutorial. (docs)
• Updated Security Tutorial. (docs)
• Updated General Assay and NAb Assay Tutorials. (docs) | (docs)

Operations

• knitr designer view. Set JavaScript dependencies to support the knitr designer view. (docs)
  === Sponsored by HIPC - Human Immunology Project Consortium
  
• Support for SQL Server 2014.
• Support for MySQL 5.6 external data sources.
• Support for building and running on Java 8.
• Removed support for PostgreSQL 8.4

Potential Backwards Compatibility Issues

• Dataset import behavior change: For consistency with other data types, imported data rows are now treated as an insert (disallowing duplicates), instead of a merge.

Highlights of LabKey Server v14.1

• Automate data processing with configurable pipeline tasks (docs)
• Untangle name and date inconsistencies across datasets and continents (docs | docs | docs)
• Collaborate in planning vaccine protocols using the study designer (docs)
• Share results conveniently with memorable, short URLs (docs)
• Intrigue new users with a visual overview and 10-minute, interactive tour (video | tour)

• Download LabKey Server 14.1
• Read the full list of 14.1 features
• Watch "sprint" videos

Data Integration

• Pipeline processing for scripts and script sequences - Simplified configuration for pipeline tasks. [docs]
  === Sponsored by Human Immunology Project Consortium (HIPC)
• Alias ParticipantIDs - Consolidate data that uses different names for the same participant/subject using alias ids. [docs]
  === Sponsored by University of Wisconsin - O'Connor Labs
• Vaccine study designer - Design vaccine-related studies for registration and data aggregation from multiple groups. [docs]
  === Sponsored by Collaboration for AIDS Vaccine Discovery (CAVD)
• Lists available in workbooks - Lists defined in a folder are visible in child workbooks. [docs]
  === Sponsored by Oregon National Primate Research Center (ONPRC)
• PostgreSQL functions in ETLs - Use PostgreSQL functions as the transform step in ETLs. [docs]

Specimen Management

• Provisioning of Specimen Tables - Improved performance for specimen archive imports.
  === Sponsored by HIV Vaccine Trials Network (HVTN)
• Admin Customizable Specimen Fields - Add and modify non-required fields in the specimen tables. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Rollup Fields in Specimen Tables - Options for storing aggregate and latest values within the specimen tables. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Customizable Specimen Email Template - Generate the most useful specimen archive notifications. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Specimen draw timestamps - Store the DrawDate and DrawTime separately to avoid erroneous conflicts when times are blank. [docs]
  === Sponsored by HIV Vaccine Trials Network (HVTN)
• FreezerPro integration support. [docs]
  === Sponsored by a major pharmaceutical corporation.

Assays

• Pipeline Assay Import - New task imports assay data using the data processing pipeline. [docs]
  === Sponsored by Human Immunology Project Consortium (HIPC)
• (Affymetrix) Import Affymetrix microarray runs from GeneTitan Excel files.
  === Sponsored by Human Immunology Project Consortium (HIPC)
• (Expression Matrix) Support for GEO series matrix TSV files. [docs]
  === Sponsored by Human Immunology Project Consortium (HIPC)
• (Flow) FlowJo 10.0.6 support. [docs]
  === Sponsored by LabKey Software
• (Luminex) Support for script to calculate positivity.
  === Sponsored by Vaccine Immunology Statistical Center (VISC)
• (NAb) Select data identifiers - When viewing NAb runs, select how you will identify the data by selecting a Participant/Visit identifier. [docs]
  === Sponsored by Vaccine Immunology Statistical Center (VISC)

Collaboration

• Updated File Browser UI - The file browser has an improved interface. [docs]
  === Sponsored by LabKey Software
• Set Date and Number Formats - Set consistent display of dates and numbers at the project- or folder-level. [docs]
  === Sponsored by LabKey Software
• Non-US Date Parsing - Set formats for parsing internationally ambiguous dates, such as 03/10/2014. [docs]
  === Sponsored by LabKey Software
• Additional security roles - Added "See Audit Log Events" and "See Email Addresses" roles. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Short URLs - Create convenient, memorable links to specific content on your server. [docs]
  === Sponsored by MacCoss Lab of Biological Mass Spectrometry

Documentation

• 10 Minute Tour - See how you can share data with researchers and colleagues. [try it]
  === Sponsored by LabKey Software
• (Video) LabKey Server Overview – A 4-minute introduction to LabKey Server. [watch]
  === Sponsored by LabKey Software
• (Video) Locate and Import Spreadsheets - Consolidate scattered spreadsheets and begin working with them in LabKey Server. [watch]
  === Sponsored by LabKey Software
• Java File Uploader - Troubleshooting documentation for the multi-file uploader. [docs]
  === Sponsored by LabKey Software
• Custom Menus - Add easy access to tools and studies in a projects. [docs]

New APIs

• saveBatches - As part of enabling multi-experiment uploads, a saveBatches() method has been added to Experiment.js, analagous to saveBatch(). [docs]
  === Sponsored by International Centers of Excellence for Malaria Research (ICEMR)
• AssayImportRunTaskType - Pipeline importer looks for output from the previous task. Imports to a selected assay database tables. [docs]
  === Sponsored by Human Immunology Project Consortium (HIPC)

Study

• Extended Study Data Model - Study products, treatments, and other support for cross study consistency. [docs]
  === Sponsored by Collaboration for AIDS Vaccine Discovery (CAVD) and the Gates Foundation
• Visit Description Hover Text - Add an optional short description to appear as hover text on visits or timepoints. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Thumbnails/mini-icons preserved on folder export/import. [docs]
  === Sponsored by Immune Tolerance Network (ITN)
• Protocol Day and Participant Visit Day - Align data across multiple studies. [docs]

Experimental Features

• New Multi-file Uploader - Upload multiple files using a drag-and-drop interface (Web-DAV based). [docs]
  === Sponsored by LabKey Software

Highlights of LabKey Server v13.3

• Gain insight across data sources by bringing data together using ETL tools (video | docs)
• Optimize specimen management with finer-grained control of allocation, export and editing (video | docs)
• Make the right reports, views and thumbnails visible to the right people (docs | docs | docs)

• Download LabKey Server 13.3
• Read the full list of 13.3 features
• Watch "sprint" videos

Data Integration

• ETL modules - Automate and streamline the assembly of data repositories from multiple sources with Extract-Transform-Load modules. ( video | docs )
• Export Charts as JavaScript - Export timecharts, scatterplots, and box charts as JavaScript for further customization. ( docs )
• Cloud Storage Integration - Manage large data files in the cloud using S3 Cloud Storage. ( docs )

Assays and 'Omics

• (Luminex) Improved quality control with single point controls in Levey-Jennings plots. ( docs )
• (NAb) New graphing layout options. ( docs )
• (MS2) Spectra library export - Export Bibliospec libraries of the spectra data associated with peptide identifications. ( docs )
• (MS2) Comet peptide search - Support for the open source Comet peptide identification search engine. ( docs )
• GEOMicroarray - Support for importing microarray data, as downloaded from GEO. ( docs )
• Flow - FlowJo 9.7.2 support

Observational Studies

• Improved Study Designer - Improved flexibility when populating values in dropdowns and creating cohorts.

Specimen Repository Management

• Introductory Video and Tutorial - Watch the video for an overview; read the tutorial for more details. ( video | docs )
• Custom Aliquots - Manage non-vial specimen types such as tissue blocks. ( docs )
• Request System Improvements - Limit which types of sites can request specimens. Customize QC flagging, comments, and groupings to easily display the sets of specimens your team needs most. ( docs )
• Export specimen settings - Export more metadata about the specimen repository and request system settings. ( docs )

UI Improvements

• Improved Views Management - Improved user interface for views and queries management. ( docs )
• Data Views Browser - The Data Views web part is available for displaying queries, reports, and views outside of a study-type folder. ( docs )
• Editable Tabs - Add, rename, move, and delete tabs for better custom project design. ( docs )
• Faceted Filters - Improved selection and filtering behavior: faceted filters respect prior filters. ( docs )

Documentation

• Improved New User Tutorials - Explore more features and get up to speed faster with updated introductory tutorials: ( docs )
• Report Permissions - New guidelines matrix for setting permissions levels on individual reports and views. ( docs )

Server Administration and Operations

• Tomcat 7 - Support for Tomcat 7. ( docs )
• PostgreSQL 9.3 - Support for PostgreSQL 9.3. ( docs )
• Audit log - Improved performance of audit log querying.
• Full-text search - Improved performance of full-text searches.
• Encrypted property store - Support for encrypted property sets. ( docs )

Installation and Upgrade

• Distribution file changes - The file structure for distribution downloads has changed in version 13.3. ( docs )
• Upgrade processing time - Note that the upgrade process for 13.3 may take longer than usual, due to audit log provisioning.
• Full-text search reindexing - The full-text search index will be regenerated after upgrading to 13.3, which can result in higher than usual indexer activity.
• GROUP_CONCAT installation - New instructions for installing/upgrading group_concat functions for SQL Server installations. ( docs )
• Proteomics Enlistment - For developers who build LabKey Server from source, the mass spectrometry binaries are now provided as a separate enlistment. ( docs )
• Module build process - For module developers, there are new options available in the module build process. ( docs )

New APIs

• Addition to R labkey package: importRows() - Provides improved performance over insertRows() for large imports. ( docs )
• New URL encoding options. ( docs )
• New SQL functions - Added functions: folderName(), folderPath(), javaConstant(), moduleProperty(), and userName(). ( docs )

Highlights of LabKey Server version 13.2

• See more of what matters with improved project and folder navigation. video | documentation
• Leverage more of your existing observational study data with REDCap integration. video | documentation
• Create elegant, dynamic R reports with the knitr visualization package. video | documentation

Resources

• Download LabKey Server 13.2
• Read the full list of 13.2 features

Observational Studies

• Study publication enhancements. Refresh data in published studies. Publish hidden datasets. Mask participant ids in lists when publishing.
• Protected health information management. Import alternate ids and date offsets.
• Data management. Improved delete behavior when browsing datasets.

Collaboration

• REDCap integration. Integrate REDCap clinical data with other data in LabKey Server.
• Improved navigation. Popup navigation menu for projects and folders.

Specimens

• Specimen aliquots. Support for vial aliquoting.
• Improved specimen workflow: Improved request customization. Faceted filtering panel. Support for tissues. Improved specimen import/export.
• Editable specimen records. User interface for editing specimen records.

Visualization

• Knitr. Create dynamic R reports by interweaving R code in HTML or Markdown pages.
• Time Charts. Improved scaling and trellising.
• Thumbnails. Autogenerate thumbnails for charts.

Assays

• (Affymetrix) Support for Affymetrix assay. Track file, sample, and other metadata for Affymetrix GeneTitan data. The data is available for downstream analysis in R or other tools.
• (Luminex) Reruns and titration exclusion. Exclude a full titration's data at once, and easily re-import corrected data.
• (NAb) Improved metadata upload. Single file upload for data and metadata in high throughput NAb assays.
• (Targeted Mass Spec) Search. Improved search by modification.
• (Targeted Mass Spec) Chromatogram Library folder type. Build collections of reference chromatograms for proteins and peptides for designing future targeted assays.
• Improved assay file import. Improved rename behavior when importing multiple files of the same name.
• Assay data archiving. Automatic archiving of files for deleted assay runs.

New APIs

• Dataset and query rename. Renamed queries and datasets are updated in custom views, reports, and query snapshots.
• Reporting API. New GetData client API lets developers chain grouping, aggregation, filtering, and more to extract data.
• Attachment field. Attachments are supported in file-based module assays.

Highlights of the 13.1 Release

• Survey Designer - Collect detailed information from collaborators, participants, and clients.
• Secure Views. Securely share client-specific views by linking data schemas across folders.
• High-throughput Assay. Support for high-throughput 384 well NAb assay.

• Download LabKey Server 13.1
• Watch video demonstrations of key features
• Read the full list of 13.1 features

Observational Studies

• Participant ID aliases. Manage alternate participant IDs from multiple sources; display and search for subjects using any of their aliases.
• Mask clinic names. Obscure clinic and draw site names when exporting or publishing.
• Date shift exclusion. Exclude selected dates from shifting on study export.
• Expanded data types for study publication. Option to include wikis, reports, webparts, properties, and other data on study publication.
• Subcategories for data views. Organize datasets and views in a hierarchy of categories.

Security

• Linked Schemas. Securely show data from one folder in another folder.
• Filtered/parameterized schemas. Refine data views by applying metadata filters and overrides to schemas templates.
• Web Part Permissions. Apply security role requirements to individual web parts.

Assays and 'Omics

• (NAb) High-throughput NAb assay. Support for high-throughput 384 well NAb assay.
• (Genotyping) Improved support for Illumina. Validate sample sheet based on Illumina indexes. Add custom fields to data exports.
• Culture adaptation assay. Create culture adaptation experiments.

Collaboration

• Survey Designer. Design web-based surveys and long form questionaires.
• Faceted filtering panel. Slide out faceted filtering panel on datasets.
• Rename and move tabs. Rename, move and delete folder tabs.

Specimen Tracking

• Request notifications configuration. Configure vial list to appear in either email body or email attachment.
• Clinic name protection. Mask clinic and draw site names with a generic label.
• Vial grouping configuration. Configure grouping hierarchy in vial browser.
• Active/inactive users highlighting. Easily identify inactive users in the specimen tracking system.

New APIs

• Updated PERL library Labkey::Query 1.03. Added ability to specify timeouts and user agent.
• Updated Query API. Added support for ExtJS 4.x store. Similar to the Ext 3.x store, in order to help with client-side component migration.

More Videos: New Feature "Sprint" Demos

Below are video excerpts from our monthly, new feature meetings. In each excerpt, a developer demonstrates the feature and takes questions from the audience. If you would like an invitation to our next "sprint" demo meeting please email sprintdemo@labkey.com.

Highlights of the 12.3 Release

• Safe Data Publication. Publish an anonymized snapshot of your data.
• Rich Assay Workflows. Data versioning provides rich data curation and precise quality control. Replace mistaken data, but retain the original data in the version history. Track assay progress and quality control, with assay progress reports.
• Targeted MS Experiments. New "Panorama" MS module supports targeted mass specrometry experiments, including integration with Skyline.

• Download LabKey Server 12.3
• Watch video demonstrations of key features
• Read the full list of 12.3 features

Study

• Study publication. Publish a secure, anonymized snapshot of your data.
• Unenrolled participant handling. Track unenrolled/pre-enrolled participants.
• Unscheduled visit handling. Allow data from unscheduled visits.
• Category hierarchy for participant groups. Organize participant groups into categories, such as "Treatment Groups" or "Treatment Regimes".

Quality Control

• Improved audit configuration. Configure auditing for any table.
• Auditing performance improvements.

Visualization and Reports

• Charting Query-based Columns. Query-based columns are available in time charts.
• Charting. Color-coded data points in scatter and box plots.

Assay

• Assay data versioning and replacement. Replace mistaken data with corrected versions. Retain previous data for auditing and data transparency.
• QC flagged progress reports. Track assay completion and quality control status on the same report. Data from unscheduled visits is also tracked.
• Support for folder move and rename.
• (ELIspot) Improved graphical calibration view.
• (Flow Cytometry) Integration with FCSExpress.
• (Mass Spec) Targeted MS Experiments. New "Panorama" MS module supports targeted mass specrometry experiments, including integration with Skyline.
• (Mass Spec) Peptide Map Export. Export combined peptide map for all runs in a comparison set.
• (Genotyping) Haplotype assignment. - Support for haplotype assignment and reporting.

Specimens

• Improved options for specimen request email notifications.
• Publish anonymized specimen snapshots.
• Ancillary study. Create an ancillary study based on a specimen request.

Administration

• Study Publishing. A suite of tools for protecting and randomizing PHI (protected health information).
• User properties. User table is now customizable.
• Custom Tabs. Support for tabbed layouts in XML-defined custom folder types.
• Graphical interface for file repository. Graphical user interface for moving and renaming files/directories in file management tool.
• Configurable tabs. Add and rename tabbed layout. Migrate child folders to child tabs.

Documentation and Samples

• New sample data. We have increased the scope of our fictional sample data set to match our growing feature set. 200+ new, imaginary human participants. New measurements (for example, viral count), new participant groups, richer visualizations.

New APIs

• Ext features. Setting for Ext 3 library delivery.
• LABKEY.MultiRequest. Note that LABKEY.MultiRequest no longer extends Ext.Observable so any Observable methods such as .addListener() will no longer work on LABKEY.MultiRequest.

Featured Videos

Developer New Feature Demonstrations

During each software development "sprint", the development team provides live demonstrations of newly minted features that have passed a full cycle of development, testing, and stabilization.  These features are ready for your inspection and use on your test servers. We're hoping to hear your feedback as we finalize our work. If you would like an invitation to our next sprint demo meeting please email sprintdemo@labkey.com

Highlights from LabKey Server version 12.2

• Quick Charts. Create a chart from a column in two clicks. Create a "best guess" chart of your data. Charts are automatically redrawn when the underlying data is filtered. Toggle between box plot/scatter plot renderings.
• Remote pipeline server installer. Easily configure a remote pipeline server with a wizard-style installer.
• Illumina support. Upload, manage, and analyze your Illumina samples.
• Folder Export/Import. Improved folder archiving includes: (1) exporting folder settings such as folder type, enabled modules, etc., (2) exporting external schema definitions, (3) allowing study archives inside of folder archives, (4) creation of folder templates.

Studies

• Participant reports. Improved user interface and data formatting.
• Dataset status. Track your study's progress by setting the status of each dataset as draft, locked, unlocked, etc. Summary table shows status of each dataset in a study.
• Faceted filtering. Filter dialog now includes data facets. Faceted filtering can be turned on or off for individual columns.
• Timepoint auto-creation. Improved behavior when automatically creating timepoint upon data import. Now set a default timepoint duration. (For date-based studies only.)
• Folder Export/Import. Improved folder archiving includes: (1) exporting folder settings such as folder type, enabled modules, etc., (2) exporting external schema definitions, (3) allowing study archives inside of folder archives, (4) support for folder templates.
• Custom thumbnail previews. Add custom preview thumbnails to the data browser.
• Participant group categories. Organize your participant groups into categories, such as Gender, Infection Status, etc.
• New "link" report type. Add a report that links to an external document or web page.
• List fields. Records in a list now include these automatically updated fields: Created, CreatedBy, Modified, ModifiedBy.

Assays

• Transform scripts. Associate multiple transform/QC scripts with an assay design. Scripts will run in series upon data upload.
• Background/unstimulated wells. (ELISpot). Subtract background noise from data using unstimulated wells as a control.
• Improved spectra count support (Proteomics). Additional options for performing the spectra count comparison, and exporting it for use in other tools.
• NAb migration tool (NAb). Migrate your NAb data from LabKey's legacy implementation to LabKey's current NAb implementation.
• Luminex curve fits (Luminex). Improved curve fit behavior makes assay quality control more efficient.
• Illumina support (Genotyping). Upload, manage, and analyze your Illumina results.
• Copy flow data to a study. (Flow Cytometry). Copy-to-study now applies to flow data.

Visualization

• Quick charts. Create a chart from a column in two clicks. Create a "best guess" chart of your data. Charts are automatically redrawn when the underlying data is filtered. Toggle between box plot/scatter plot renderings.
• Box plots. Chart the quartile distributions. Outliers are shown as data points. Cohorts and participant groups are included as options for the X axis.
• Scatter plots. Chart correlations in your data. Edit the radius, color, and opacity of data points.
• Time charts. New look and feel for the chart editing environment: (1) popup dialog boxes, (2) edit axis properties directly from chart, (3) updated filter panel, (4) "View Mode" hides the editing buttons. Refactored to use the new charting API -- see the API section below for details.
• Links from data points. Developers can add a function to be called when a data point is clicked.
• New Charting API / JavaScript Libraries. See the API section below for details.

Pipeline

• Remote pipeline server installer. Easily configure a remote pipeline server with a wizard-style installer.

Security

• Impersonate roles. Impersonate security roles in addition to impersonating security groups and individual users.
• Auditing. Dataset export events (including filter information) can be viewed in the audit log.

Specimens

• sampleminded support. Import specimen data in the sampleminded format.
• Specimen search/requests. Users can now select multiple items simultaneously from dropdown menus.
• Specimen request notification. Set default notification behavior when specimens are requested from the repository.
• Specimen import. Build a specimen request by uploading a file containing specimen ids.

Search

• Full-text search for lists. Customizable indexing of list data and metadata.

New APIs

• Charting API. New graphics API combines the D3 and Raphael javascript libraries.
• Ext 4.1.0. LabKey Server now uses Ext 4.1.0.
• Declaring dependencies. New mechanism for declaring script dependencies.
• LabKey SQL improvements. GROUP_CONCAT aggregate function support on Microsoft SQL Server and ability to specify custom delimiters.
• Tighter security on some core queries. Previously, all authenticated users (non-guests) were able to see data in the core.members and core.principal queries. These are now restricted to users with Admin permissions.

Related Links

• Download LabKey Server version 12.2
• Learn What's New in 12.2

These videos demonstrate key features from the 12.2 release of LabKey Server.

To view these videos in full screen, click the icon in the lower right as the video plays.

• Assessing Data with Quick Charts
• Study Administration: Organizing Data

Assessing Data with Quick Charts

Shows how to quickly assess the meaning of new data using Quick Charts.

Study Administration: Organizing Data

Shows how to organize your study data, such as setting the status and category for documents.

Highlights of the 12.1 Release

• Customizable Participant Reports. Create exportable reports focusing on selected participants and data. (See a video demonstration.)
• Participant Lists. Get to your participant data quickly with faceted filtering. (See a video demonstration.)
• Permissions Reports. See who has access with detailed permissions reports. (See a video demonstration.)