LabKey Server

LabKey Server is an enterprise-capable, web-based platform for organizing, analyzing, and securing laboratory and clinical research data. Built around projects and folders, it consolidates assay results, sample inventories, study datasets, and files into a single searchable environment with built-in audit logging, row/column security, and PHI controls. The product family includes Sample Manager, LabKey LIMS and Biologics modules that add specialized sample tracking, LIMS workflows and biologics-centric metadata, and is available in Community and Premium editions (plus trial hosting via LabKey Cloud). At its core LabKey Server supports structured import and curation of experimental data: assay designs can be inferred from spreadsheets, transformed with user scripts, and bulk-imported while preserving provenance. The platform provides dataset QC states, guide sets and QC reports for assays such as Luminex, neutralizing antibody (NAb) assays and flow cytometry, with features to track controls, generate Levey–Jennings plots and compare standard curves across runs. Samples and their lineage are first-class entities — you can register sample types, track derivation/parents, tag and barcode items, and map storage locations in freezers. Linking samples to assays and studies enables integrated longitudinal analysis and traceability from raw instrument outputs to study endpoints. LabKey also includes robust automation and ETL capabilities. The Script Pipeline and ETL framework support scheduled or file-watcher–triggered workflows, transformation scripts in R or Python, and parallel pipeline runs when needed. Integration with message brokers such as ActiveMQ is supported for scaling pipelines. Developers and power users can extend the platform with Java modules, JavaScript-based web parts, server-side transformation scripts, and REST/ODBC/JDBC access. There are premium developer resources and examples for creating custom buttons, invoking scripts from the UI, exporting data grids as scripts, and embedding visualizations (Spotfire, Plotly) or R reports into pages. For analysis and reporting, LabKey provides embedded R reports and integrations with RStudio, plus API demos for Python and other clients. You can fetch LabKey data programmatically, render Plotly or Spotfire visualizations, export grid data for downstream analytics, or run server-side calculations to display calculated columns in queries. External schemas and database connections (including MS SQL Server) are supported; the product can sit alongside institution systems (EHR, Medidata/CDISC ODM) and consume or publish data to cloud storage and instrument systems. Security features include configurable permissions at the report, chart and grid level, row- and column-level protections for sensitive fields, CSRF protection, audit logs, project locking and electronic signatures to support compliance workflows. Typical use-cases range from academic labs wanting a single place to store and version experimental data, to translational and pharma teams running sample management and LIMS workflows across multiple groups, to clinical studies that require PHI handling, audit trails and exportable datasets. Administrators can export/import projects and folder settings, configure data retention and encryption keys, and tune the stack for cloud or on-prem deployments (Docker TLS, recommended reference architectures, and AWS firewall guidance are provided). Support and documentation vary by edition: Community Edition offers self-service docs and community support, while Premium Editions provide private support portals, phone/video help, and premium documentation and code samples for complex integrations and deployment tasks. Because LabKey is modular and API-driven, teams can start with the Community Edition or a hosted trial and extend the platform incrementally — adding Sample Manager for inventory and chain-of-custody, enabling LIMS features for lab workflows, or adopting Biologics modules for molecule and assay batch management. The platform’s combination of data modeling, ETL/pipeline automation, developer APIs, and governance features makes it well suited for organizations that need reproducible, auditable data management across assays, instruments and studies.