LabKey Server
| Developer(s) | LabKey Software Foundation |
|---|---|
| Stable release |
16.3[1] / November 14, 2016
|
| Development status | Active |
| Written in | Java |
| Operating system | Cross-platform |
| License | Apache License 2.0 |
| Website | http://www.labkey.org |
LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline.
Contents
License[edit]
The LabKey Software Foundation licenses LabKey Server and its documentation for free under the Apache License.[2]
Languages and extensibility[edit]
The base platform is written in Java. It can be extended through the addition of Java-based modules or simple, file-based modules written in HTML, XML and JavaScript.[3] The platform can also be extended using LabKey Server's Java, JavaScript, R, Python, Perl and SAS client libraries.[4]
History[edit]
LabKey Server was spun out of the Computational Proteomics Lab at the Fred Hutchinson Cancer Research Center after contributors realized that the software could be beneficial to the broader scientific community. The software was originally called the Computational Proteomics Analysis System (CPAS).[5][6][7]
Features[edit]
LabKey Server provides a secure data repository for all types of biomedical data, including mass spectrometry, flow cytometry, microarray, microplate, ELISpot, ELISA, NAb and observational study information. A customizable data processing pipeline allows the upload and processing of the large data files common in biomedical research.
The platform also provides domain-specific support for several areas of research, including:
- Observational Studies. Supports management of longitudinal, large-scale studies of participants, subjects or animals over time. Allows the integration of clinical data with assay results.
- Proteomics. Allows the processing of high-throughput mass spectrometry data using tools such as the X! Tandem search engine, the Trans-Proteomic Pipeline, Mascot and Sequest. Certified as "Silver-Level Compliant Data Service" with the caBIG standard.
- Flow Cytometry. Supports automated quality control, centralized data management and web-based data sharing. Integrates with FlowJo.
Users[edit]
Users range from individual labs to large research consortia. In 2010, the program's users included the following:[8]
- Fred Hutchinson Cancer Research Center
- Statistical Center for HIV/AIDS Research and Prevention (SCHARP)
- Center for HIV-AIDS Vaccine Immunology (CHAVI) at Duke University
- Collaboration for AIDS Vaccine Discovery (CAVD), funded by the Gates Foundation
- Wisconsin National Primate Research Center
- International AIDS Vaccine Initiative (IAVI)
- Infectious Disease Research Institute (IDRI)
- Cedars-Sinai Medical Center
- Institute of Molecular and Cell Biology (Singapore)
- NIMML
- Harvard Partners
- University of Washington
- University of Michigan
- University of Kentucky
- University of Wisconsin
Publications[edit]
- Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark (2011). "LabKey Server: An open source platform for scientific data integration, analysis and collaboration". BMC Bioinformatics. 12: 71. doi:10.1186/1471-2105-12-71. PMC 3062597
. PMID 21385461. - Rauch, Adam; Bellew, Matthew; Eng, Jimmy; Fitzgibbon, Matthew; Holzman, Ted; Hussey, Peter; Igra, Mark; MacLean, Brendan; et al. (2006). "Computational Proteomics Analysis System (CPAS): An Extensible, Open-Source Analytic System for Evaluating and Publishing Proteomic Data and High Throughput Biological Experiments". Journal of Proteome Research. 5 (1): 112–21. doi:10.1021/pr0503533. PMID 16396501.
- Shulman, Nicholas; Bellew, Matthew; Snelling, George; Carter, Donald; Huang, Yunda; Li, Hongli; Self, Steven G.; McElrath, M. Juliana; De Rosa, Stephen C. (2008). "Development of an automated analysis system for data from flow cytometric intracellular cytokine staining assays from clinical vaccine trials". Cytometry Part A. 73A (9): 847. doi:10.1002/cyto.a.20600.
- "The Best of Both Worlds: Integrating a Java Web Application with SAS Using the SAS/SHARE Driver for JDBC" (PDF).
References[edit]
- ^ "Release: LabKey Server v16.3". Retrieved 2016-11-14.
- ^ "LabKey Frequently Asked Questions: /home". Labkey.org. Retrieved 2010-05-29.
- ^ "Building Modules: /home/Documentation". Labkey.org. Retrieved 2010-05-29.
- ^ "LabKey API: /home/Documentation". Labkey.org. Retrieved 2010-05-29.
- ^ "Computational Proteomics Laboratory". Proteomics.fhcrc.org. Retrieved 2010-05-29.
- ^ http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html
- ^ "Center News - 1/5/06 - Center, NCI launch open-source software for proteomics analysis". Fhcrc.org. 2006-01-05. Retrieved 2010-05-29.
- ^ "Our Clients | LabKey Software". Labkey.com. Retrieved 2010-05-29.
External links[edit]
- LabKey Server. The official web site for the LabKey Software Foundation includes documentation and community support forums.
- LabKey Software. LabKey Software provides professional customization and support for LabKey Server.
