LabKey Server

Research's most flexible platform for scientific insight

LabKey Server

LabKey Server is an open-source software platform designed to help organizations integrate, analyze, and share complex biomedical data. Adaptable to varying research protocols, analysis tools, and data sharing requirements, LabKey Server couples the flexibility of a custom solution with enterprise-level scalability and support.

Make Sense of Diverse Data

Data has the power to fuel discovery, but it is much more challenging to achieve when data is scattered across systems, spreadsheets, and files. LabKey Server brings together data of all types to assemble a full picture of disease patterns, mechanisms, and treatment responses.

Securely Connect Dispersed Teams

Many of the most promising research opportunities require large-scale teamwork, but these types of dispersed collaborations present a variety of data security and communication challenges. LabKey Server provides teams with a web-based portal for sharing and accessing data, equipped with a robust role-based permissions model to ensure security and connect the right team members to the right data.

Achieve High Quality Data, Faster

Today’s complex research environment often means teams end up spending more time managing data than analyzing it. LabKey Server provides a flexible workflow and integration framework to standardize and automate processes, helping reduce the time spent on error-prone manual data management tasks.

Adapt to Evolving Needs

Rapid innovation drives scientific progress and organizations must be prepared to adapt to the ever changing needs of research. LabKey Server is built on a flexible, developer friendly framework that is designed to scale and evolve with research, helping users stay on the leading edge of biomedicine.

Assemble a unified view of diverse data with LabKey Server’s flexible data integration tools.

Assay Data

LabKey Server recognizes many instrument-specific data and metadata files, and provides specialized functionality to help users get the maximum insight from each data type. Specialized assays and tools are available for Mass Spectrometry, Sequencing, Flow Cytometry, Luminex®, and more.

LabKey Server also supports all common tabular file types including Excel formats (XLS, XLSX), Comma Separated Values (CSV), and Tab Separated Values (TSV). To integrate any novel data, LabKey Server provides a general purpose assay type that is defined by the user.


LabKey Server file repositories provide a centralized location where structured and unstructured files can be securely searched, shared, and viewed. Structured data files can be imported into the database for integration with related data and analysis using LabKey Server’s visualization and reporting tools. Both structured and unstructured files can also be tagged with metadata to increase their discoverability. 

Study Data

Integrating clinical and demographic data for participants, cohorts, and groups into LabKey Server allows users to connect study data with related assay and specimen data.

Specimen Information

LabKey Server can act as the database of record for specimens, allowing you to import, enter, and edit specimen information within the system, or as the integration point for information from external system like FreezerPro. Specimen information can be integrated with related assay or study data for analysis.

Electronic Data Capture

LabKey Server supports the direct collection of data through native survey tools as well as integration with external electronic data capture tools like REDCap. LabKey Server can also serve as a back end data repository and analysis tool for data gathered through ResearchKit®- and ResearchStack-based mobile applications.*

Flexible Integration Methods

There are a variety of methods for integrating data into LabKey Server, allowing users to centralize data without disrupting their existing workflows. Data can be pulled into LabKey Server via direct connection to instruments, added manually through file uploads or data entry tools, or imported programmatically through ETLs. Data stored outside of LabKey Server can also be accessed via external schemas.

*Mobile application integration is currently in-development, read more.

Uncover trends and data of interest with LabKey Server’s data exploration and analysis tools.

Visualization & Reports

LabKey Server provides a variety of ways to visually display data, helping users discover meaningful trends more quickly. The platform supports simple column visualizations and calculation of column aggregates for single datasets as well as more complex charts, JavaScript reports, query snapshots of integrated data.


LabKey Server serves as a full-featured SQL engine that allows you to securely query integrated data, easily join data across tables and connect to and work with data in external schemas. Queries can be be saved for future use or shared with collaborators.

External Analysis

LabKey Server data can be easily exported in common formats that can be consumed by external analysis applications (e.g., Excel). The platform also integrates with the R statistical programming environment to analyze and visualize datasets. The results of R scripts can be displayed in LabKey reports that reflect live data updated every time the script is run.

Securely collaborate across teams, organizations and geographies using LabKey Server's tools for web-based collaboration.

Editable Web Pages

LabKey Server wikis provide a simple way to document and contextualize your project. Wikis are easy to edit web documents that can be collaboratively maintained by multiple users. These pages can house house text, images, links, and even live data. Users can also convert wikis to HTML pages for more in-depth customization.

File Sharing

In many lab environments, research files end up scattered across many different computers and shared with team members via email which can lead to duplication and confusion. LabKey Server file repositories provide a secure, web-based method for storing, sharing, viewing and downloading research files.

Message Boards

Commonly used for announcements, discussions of on-going work, and providing support, message boards in LabKey Server allow users to share information with collaborators in a threaded format.

Web-Based Portals

LabKey Server can be used to create web-based workspaces where teams can collaboratively maintain data, manage team processes, and communicate securely. Utilizing the platform’s fined-grained permissions model, access to web portals can be easily restricted to members of the working group.

Centrally manage research workflows from common lab tasks to unique organizational processes with the LabKey Server platform.

Specimen Requests

The LabKey Server specimen request system manages the allocation and transfer of scarce specimen resources between sites. The underlying workflow that supports the request and approval process is highly customizable, giving users control over which vials are available, who has access to the repository, and the stages of the process.

Assay Request Tracking*

LabKey Server’s assay request tracking system allows management and reporting of work requests and data uploads, seamlessly tying them together to allow for navigation between the request system and the analytical data generated. This tool includes an easy-to-deploy template for managing assay requests that can be customized to support lab-specific workflows.

Issue Tracking

LabKey Server provides a centralized workflow system for tracking issues and tasks, helping teams manage projects more effectively. Users can use LabKey Server issue trackers to assign tasks to themselves or others, and follow the task through the work process from initiation to completion.

Free-Text Abstraction

LabKey Server provides an annotation and task management pipeline to manage the stages of the document abstraction and review process. This workflow tool ensures consistency and security of data being processed by standardizing tasks, automating assignment, and restricting access to data based on users’ roles in the abstraction process. Currently, this workflow tool supports manual abstraction, but future phases of development will introduce the use of Natural Language Processing engines to further accelerate the annotation process.

Custom Workflows

Utilizing LabKey Server’s integration with the Activiti business process management platform, developers can create custom workflows to standardize and streamline essential research processes. Activiti supports a variety of tasks and workflows within LabKey Server, including user tasks for manual data manipulation, decision gates for if-then-else implementation and timer tasks that trigger other tasks on a schedule or after a certain amount of time. These workflows can be used to manage all types of lab and clinical functions from assay requests to diagnosis adjudication.

*Assay Request Tracking is currently in-development.

Protect sensitive research data and increase visibility into data usage with LabKey Server’s robust security model.

Security Groups

LabKey Server uses a group and role-based security model to manage user permissions and enable selective sharing of information to different users. Teams can utilize pre-configured, standard security roles for easy administration or create custom security groups to support specialized access levels.


LabKey Server supports several models of user authentication to meet the varying security requirements of different organizations. The platform supports authentication using LabKey Server-managed credentials as well as lightweight directory access protocol (LDAP), single sign-on (CAS and SAML) and two-factor authentication (Duo).

Regulatory Compliance

LabKey Server includes a variety of facilities to ensure regulatory compliance for teams managing protected health information. Security features include collection of user declarations of role, IRB, PHI level and terms of use prior to access, dynamic PHI redaction and shifting based on PHI level, restriction of export and external API access, and detailed logging of all patient record access including executed SQL plus patient IDs and PHI accessed.

LabKey offers Premium Editions of LabKey Server that include support from our experienced professional software engineers to ensure successful configuration of LabKey Server to support HIPAA and FISMA compliance.

Unlock the power of the LabKey Server platform with hands-on training and professional services delivered by LabKey experts.


LabKey provides all users access to extensive documentation to help support the installation, administration, and usage of LabKey Server.


LabKey Server can be hosted by LabKey in a cloud-based environment or deployed locally for groups that require full hosting control. LabKey offers operations consulting services to help guide the installation and maintenance of self-hosted solutions.


Hands-on training for users and administrators, and developers is offered to premium LabKey Server subscribers. Training sessions are customized for each client, and conducted by LabKey’s dedicated trainers.

Custom Development

LabKey offers custom development services to clients who would like to extend LabKey Server beyond existing functionality. Custom development is professionally maintained and supported by the LabKey team, ensuring its long-term usefulness.

Visit the LabKey Support portal for LabKey Server documentation, tutorials, and community forums.

Applications of LabKey Server

LabKey Server can be used to overcome a wide variety of challenges for biomedical research groups. Common applications of LabKey Server include:

Centralized Data Storage

Centralized Network Data Management

Use LabKey Server to integrate and centrally store data generated by multiple teams, easing operations and opening the door to deeper insight.

Read the Atlas case study to learn more about using LabKey Server for centralized data management. 

data exploration portal

Data Visualization Portals

Provide a portal for exploration of integrated data to users without compromising PHI using LabKey Server’s data integration, visualization and security features.

Read the Argos case study to learn more about using LabKey Server to create data visualization portals. 

public data sharing

Public Data Sharing

Provide direct access to research datasets post-publication or in real-time to promote transparency and collaboration. 

Read the ITN Trial Share case study to learn more about using LabKey Server for public data sharing. 

Primate Colony Management

Primate Colony Management

Manage clinical records, connect them with project- or investigator-specific research data, and do comprehensive reporting on individual animal or across the enter colony using LabKey Server for primate colony management.

Read the Primate EHR case study to learn more about using LabKey Server for primate colony management. 

LabKey Server Editions

LabKey Software offers multiple Editions of LabKey Server and a suite of Add-Ons to best meet different levels of need for support and functionality.

Community Edition

Intended for: Evaluators, technical enthusiasts, and teams with substantial in-house development resources.

Service Level: Documentation, Tutorials, and Community Forums. No formal support provided.

Pricing: Free

Professional Edition

Intended for: Teams that want to optimize workflows, enable collaboration and support basic connection of lab, specimen and clinical data, but do not need deep integration with other systems or major customization.

Service Level: Customized training for users and administrators, on-going project management, data management, scripting (R and SQL), security, and administration guidance, private support portal, priority fixes for client specific issues.

Pricing: Annual subscriptions starting at $37k/ year

Professional+ Edition

Intended for: Teams that seek to integrate LabKey Server with external systems, manage a larger installation, and/or build custom solutions that extend LabKey Server.

Service Level: Includes all Professional Edition services, plus ongoing system architecture and design guidance from technical leads, support for multi-organization portals, advanced developer support including server to server integrations, client APIs, ETLs, assay transform scripts, remote pipeline processing servers and clusters, custom LabKey-based pipelines, and module development assistance.

Pricing: Annual subscriptions starting at $70k/ year

Enterprise Edition

Intended for: Teams that need to support clinical data integration at large scale, potentially including regulatory compliance.

Service Level: The advanced technical support provided with the Enterprise Edition of LabKey Server tailored to meet the needs of each Enterprise edition client.

Pricing: Contact for pricing