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LabKey Server is an open-source web platform for integrating, analysing and sharing biomedical research data. The company behind it, LabKey, also sells laboratory software built around that platform, including LIMS, sample management and electronic lab notebook products. (Not to be confused with labkey.io, an unrelated electronic door-control company.) This page separates the open-source core from the commercial product line and points to the official documentation. Facts below were read from LabKey’s own pages, its public code repository and a peer-reviewed paper on 2026-11-07.
What is LabKey?
LabKey’s documentation describes the platform as providing “an integrated data environment for biomedical research.” The core software, LabKey Server, is published as a set of modules in the LabKey/platform repository on GitHub under the Apache License 2.0. The repository describes itself as “a set of modules that provide core functionality for LabKey Server.”
The design was described in a peer-reviewed paper: Nelson EK et al., “LabKey Server: An open source platform for scientific data integration, analysis and collaboration,” BMC Bioinformatics 2011;12:71 (doi:10.1186/1471-2105-12-71). It reports that the platform was built for large collaborative HIV research programmes and lists these capabilities: specimen request and tracking, graphical assay design, data integration through shared identifiers and lookups, permission-aware queries through a point-and-click interface or SQL with export, access to external databases (PostgreSQL, MySQL, SQL Server, SAS), client libraries (JavaScript, Java, R, SAS, Perl, and JSON over HTTP), built-in R scripting, role-based security with LDAP and single sign-on, and audit logging.
Who runs LabKey and what does it cover?
LabKey (labkey.com) states it has operated since 2003 and describes itself as a provider of LIMS and data-management software for labs. Its site lists these products: Sample Manager, LabKey LIMS, Biologics LIMS, an electronic lab notebook (ELN), a scientific data management system (SDMS), EDC (electronic data capture), Panorama (for mass spectrometry data, associated with the Skyline tool), and LabKey Cloud. It also offers a Community Edition download. The company says more than 500 labs and research organisations run on LabKey (a vendor statement, not independently verified) and lists pharma and biotech, academia, government, agriculture, food and beverage, environmental and veterinary sectors.
The open-source core and the commercial products are different things. The Apache-licensed repository is the platform; the named products are LabKey’s offerings built around it. This page does not state which features belong to which edition, because LabKey’s own pages are the authority for that split, and it gives no pricing.
Scale in the published literature
The 2011 paper’s case study of the Atlas HIV research environment reported about 2,800 user accounts and about 27,000 assay runs at the time of writing. These are historical figures from the paper, not current usage numbers.
How do I explore the platform documentation?
The public documentation lives at labkey.org under Documentation. Its Getting Started page organises the basics under these terms, which are the interface vocabulary to look for:
- Open the Documentation area on labkey.org and choose Getting Started.
- Read the Projects and Folders pages, and the Folder Types page, to see how data is organised and secured.
- Learn Data Grids: sorting, filtering, customising views and exporting.
- Use the Filter Data page for column filters on a grid.
- Move to SQL Queries: Create a SQL Query, the LabKey SQL Reference, and the SQL Query Browser.
- For the open-source side, see the Open Source Project section of the documentation and the LabKey/platform repository.
- To cite the software in a paper, use LabKey’s own “How to Cite LabKey Server” page; the 2011 BMC Bioinformatics paper above is the published reference describing the platform.
Sign-in for a deployed LabKey Server is provided by whichever institution or vendor hosts it; this page does not cover login.
Strengths and limits
What the sources support
- Open core: Apache 2.0 licensing means the platform code can be inspected in the public repository.
- Integration: the paper describes joining assay, specimen and clinical-style data through shared identifiers and querying it under role-based permissions with audit logging.
- Scriptability: SQL, built-in R scripting and client libraries allow analysis to be reproduced outside the web interface.
Limits to plan for
- The 2011 paper describes an early version; check current documentation for present features.
- Commercial edition boundaries, current version numbers and pricing are set by LabKey and are not covered here.
- Whether a deployment meets regulated-lab requirements depends on how it is validated and configured. See the CASRAI guide to GMP LIMS for the general framework.
Alternatives and where to read next
| If you need | Read |
|---|---|
| A plain explanation of what a LIMS is | What is a LIMS system? |
| Other open-source LIMS options (SENAITE, OpenELIS) | Open-source LIMS: SENAITE and OpenELIS |
| Connecting a LIMS to instruments and other systems | LIMS integration |
| Sample tracking products compared | Sample management software comparison |
| The distinction between lab and clinical systems | LIMS vs LIS |
For funder expectations on data sharing, which platforms like this help meet, see data management plan (DMP).
FAQ
Is LabKey free and open source?
The LabKey Server platform code is published under the Apache License 2.0 on GitHub (LabKey/platform). LabKey also sells commercial products and offers a Community Edition download; consult labkey.com for the terms of each.
What is LabKey used for?
According to its documentation and the 2011 paper, it integrates and analyses biomedical research data, including assay results and specimens, with SQL queries, R scripting and role-based access.
Is LabKey the same as labkey.io?
No. labkey.io is an unrelated company that makes electronic door-control products. The research platform is at labkey.com and labkey.org.
How do I cite LabKey?
Use LabKey’s own “How to Cite LabKey Server” documentation page. The 2011 paper (Nelson et al., BMC Bioinformatics 12:71) describes the platform.
Sources
- LabKey, company site, https://www.labkey.com/ (read 2026-11-07).
- LabKey documentation, Getting Started, https://www.labkey.org/Documentation/wiki-page.view?name=gettingStarted (read 2026-11-07).
- LabKey/platform repository, https://github.com/LabKey/platform (read 2026-11-07).
- Nelson EK et al. BMC Bioinformatics 2011;12:71, https://pmc.ncbi.nlm.nih.gov/articles/PMC3062597 (read 2026-11-07).
