LabKey Server
Open Source Freedom, Enterprise Quality
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.
Explore LabKey Server free for 30-days.
One Flexible Platform, Countless Research Solutions
Assay Data Integration
Integrate experiment data and metadata from proteomics, genomics, flow cytometry, and other high-throughput assays.
Longitudinal Study Data Management
Connect clinical, demographic, experimental data from study participants to create a complete dataset for analysis.
Population Health Research
Create an aggregated view patient data for exploration without compromising patient privacy.
Biologic Research & Development
Optimize R&D efforts through centralized management of entity, sample, assay, and media data.
Research Network
Data Centralization
Extend collaboration efforts beyond your organization while maintaining data security.
Clinical Document Abstraction
Automate workflows for more efficient abstraction, processing, and validation of free-text data.
Targeted Mass Spectrometry Repository
Central Skyline documents to support iterative methods development.
Trusted by More Than 500 Research Organizations Worldwide
LabKey Server Technology
Open Source Core: The core functionality of the LabKey Server platform is open source and freely available. API
API Accessible: Extend and customize LabKey Server to meet you unique needs using the LabKey Server client APIs.
Developer Friendly: Create your own LabKey Server modules to support to accomplish specific research objectives.
Enterprise Scalability: Manage large quantities of data without losing performance quality.
Core Features
Assemble a unified view of diverse data with LabKey Server’s flexible scientific 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. To integrate any novel data, LabKey Server provides a general purpose assay type that is defined by the user. The general purpose assay type supports assay data in all common tabular file types including Excel formats (XLS, XLSX), Comma Separated Values (CSV), and Tab Separated Values (TSV).
Learn more about assay data integration >
Files
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 the software’s built-in 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 the software platform 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.
Learn about LabKey developer tools >
Learn more about LabKey instrument, software, and database integrations >
*Mobile application integration is currently in-development, read more.
Uncover trends and data-driven insights 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. Learn more about data visualization tools >
Querying
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
The LabKey Server software platform 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.
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.
Authentication
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.
Documentation
LabKey provides all users access to extensive documentation to help support the installation, administration, and usage of LabKey Server.
Hosting
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.
Training
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.
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.
LabKey Server Editions
LabKey offers multiple Editions of LabKey Server and a suite of Add-Ons to best meet different levels of need for support and functionality. Compare server editions.
Compare LabKey Server Editions
| Community Edition | Professional Edition | Professional Plus Edition | Enterprise Edition | |
|---|---|---|---|---|
| General | ||||
| Base LabKey Server Feature Suite | X | X | X | X |
| Access to Source Code and Installers | X | X | X | X |
| Custom LabKey Server Distribution | X | X | X | |
| Extended Look-and-Feel Customization | X | X | X | |
| Groups Supported Within Organization | Single | Single | Multiple | |
| Cloud Hosting | Add-On | Add-On | Add-On | Add-On |
| Data Processing | ||||
| Base LabKey Server Pipelines (e.g. Mass Spectrometry, Flow Cytometry) | X | X | X | X |
| Automatic Pipeline Triggers upon File Availability | X | X | X | |
| Document Abstraction Workflow and Curation System | X | |||
| Natural Language Processing Pipeline | X | |||
| Authentication | ||||
| Built-In Database and LDAP Authentication | X | X | X | X |
| Single Sign-On Protocols: CAS, Google OAuth, SAML | X | X | X | |
| Two-Factor Authentication via Duo | X | X | X | |
| HIPAA, FISMA, CFR Part 11 Compliance Support | ||||
| Electronic Signatures | X | X | ||
| Advanced Account Management | X | X | ||
| Dynamic Terms of Use | X | X | ||
| Managed Access to PHI/PII Based on Security Roles | X | X | ||
| Logging of all PHI/PII Accesses and User Assertions | X | X | ||
| Direct Integration | ||||
| RStudio | X | X | ||
| REDCap | Add-On | X | X | |
| FreezerPro | Add-On | X | X | |
| Amazon Redshift | Add-On | X | X | |
| Spotfire via JDBC | Add-On | X | X | |
| File Management with Amazon S3 | Add-On | X | X | |
| Training | ||||
| Online Documentation, Tutorials, Videos and Community Forum | X | X | X | X |
| Custom-Tailored Training for Users/Administrators | X | X | X | |
| Custom-Tailored Training for Developers | X | X | ||
| Support | ||||
| Access to Public Forums & Documentation | X | X | X | X |
| Priority Fixes and/or Investigation of Client-Reported Bugs | X | X | X | |
| On-Going Maintenance of Client-Funded Features | X | X | X | |
| Private Support Portal | X | X | X | |
| Regular Meetings with Dedicated Account Manager | Monthly | Weekly | Weekly + | |
| Installation, Maintenance, Monitoring, Reporting, and Upgrade Assistance | X | X | X | |
| Hardware, Software, Security, and Data Management Recommendations | X | X | X | |
| System Architecture and Design Advice from Development Leads | X | X | ||
| Development Recommendations, Code Reviews, and Troubleshooting | X | X | ||
LabKey Cloud Services
LabKey cloud services significantly reduce the operations burden of using LabKey Server and help ensure a reliable, up-to-date operating environment for users. Teams using LabKey cloud services to host their LabKey solutions receive professionally managed upgrades to the all major releases of LabKey Server and back-ups of their environments.