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

Elizabeth K Nelson1, Britt Piehler, Josh Eckels

  • 1LabKey Software, Seattle, WA 98102, USA. eknelson@labkey.com

BMC Bioinformatics
|March 10, 2011
PubMed
Summary
This summary is machine-generated.

LabKey Server enhances collaborative disease research by providing integrated data and specimen management tools. This open-source platform supports secure data sharing, analysis, and visualization for global research consortia.

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Area of Science:

  • Biomedical research
  • Computational biology
  • Data science

Background:

  • Broad-based collaborations are common in disease research, exemplified by the Global HIV Enterprise.
  • Coordinated research across institutions, continents, and specialties requires advanced data and specimen management tools.
  • Current tools must facilitate organization, integration, standardization, and secure collaboration for heterogeneous data.

Purpose of the Study:

  • To enhance the LabKey Server platform (formerly CPAS) to meet the needs of large-scale, cross-institutional research collaborations.
  • To provide a freely available, open-source software solution for managing diverse research data and specimens.

Main Methods:

  • Enhanced LabKey Server with features for specimen request submission across organizations.
  • Implemented graphical definition of experimental data types, metadata, and data collection wizards.
  • Enabled transition of experimental results from spreadsheets to a shared database.
  • Integrated secure organization, analysis, visualization, and sharing of diverse data types.
  • Added capabilities for dynamic interaction with external data sources, participant tracking, custom interface development, and R scripting for visualizations.

Main Results:

  • The enhanced LabKey Server, exemplified by the Atlas installation, supports consortia within the Global HIV Enterprise.
  • Atlas has over 2,800 active users from ~36 countries and 350 organizations.
  • Atlas tracks ~27,000 assay runs, 860,000 specimen vials, and 1,300,000 vial transfers.
  • Diverse research organizations have adopted and adapted LabKey Server for collaborative research.

Conclusions:

  • Sharing data, analysis tools, and infrastructure accelerates research consortia efforts by improving efficiency and enabling novel insights.
  • The Atlas installation demonstrates the effectiveness of the LabKey platform for collaborative research.
  • Stable, supported builds of LabKey Server are freely available, with documentation and source code under the Apache License 2.0.