LabKey Server: An Open Source Platform for Large-Scale, Translational Research

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Presented at the 2013 BioITWorld Conference, April 9-11, 2013


Peter Hussey, Elizabeth K. Nelson, Britt Piehler, Matthew Bellew, Mark Igra, Josh Eckels, Adam Rauch


Translational research networks engaged in large-scale, collaborative projects face difficult data management challenges. To speed progress towards disease therapies, researchers need software systems that provide robust support for not just clinical and specimen data, but also the complex information produced by modern molecular and cellular techniques. These data sets must be gathered from often geographically distributed labs, screened for quality and consistency, linked with curated public data sources, and shared across the network. Statistical and visualization tools must be able to access the combined data as a basis for forming and testing translational hypotheses. Upon publication, the software system should offer public access to the data, metadata, and tools such that independent reviewers can reproduce the research results– a crucial requirement for the advancement of translational science.

LabKey Server stands out as an open source system that meets these challenges. LabKey Server offers a robust and flexible platform for diverse data integration, secure sharing, direct access from statistical and visualization tools, and assay data annotation for establishing provenance of results. These capabilities make LabKey Server a valuable tool that helps project teams discover insightful answers to translational research questions. LabKey Server’s data storage and query capabilities, assay framework, secure accessibility across the internet from tools and scripts as well as browsers, all combine to make the platform an important asset to translational research projects. Its usefulness extends beyond the research phase to publication, where the same capabilities support reproducibility of results by independent reviewers.

Since its launch in 2005, this open source system has been adopted and customized by organizations across the globe, including the Immune Tolerance Network and consortia within the Global HIV Enterprise. As of early 2013, over 70 active installations of LabKey Server leverage more than $15 million of past investment in the platform. Source code, compiled binaries, documentation, and tutorials are professionally maintained by LabKey and freely available under the Apache 2.0 license for download.