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Open Access Highly Accessed Software

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

Elizabeth K Nelson1*, Britt Piehler1, Josh Eckels1, Adam Rauch1, Matthew Bellew1, Peter Hussey1, Sarah Ramsay2, Cory Nathe2, Karl Lum1, Kevin Krouse1, David Stearns1, Brian Connolly1, Tom Skillman2 and Mark Igra1

Author Affiliations

1 LabKey Software, Seattle, WA, 98102, USA

2 Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA

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BMC Bioinformatics 2011, 12:71  doi:10.1186/1471-2105-12-71

Published: 9 March 2011

Abstract

Background

Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely.

Results

To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment.

Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers.

Conclusions

Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org webcite. Documentation and source code are available under the Apache License 2.0.