LabKey Server
Encyclopedia
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.
.
. It can be extended through the addition of Java-based modules or simple, file-based modules written in HTML
, XML
and JavaScript
. The platform can also be extended using LabKey Server's Java, JavaScript
, R
, Python
, Perl
and SAS client libraries.
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).
, 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:
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
, open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
software available for scientists to integrate
Data integration
Data integration involves combining data residing in different sources and providing users with a unified view of these data.This process becomes significant in a variety of situations, which include both commercial and scientific domains...
, analyze
Data analysis
Analysis of data is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making...
, and share
Data sharing
Data sharing is the practice of making data used for scholarly research available to other investigators. Replication has a long history in science...
biomedical research data. The platform provides a secure data repository
Information repository
An information repository is an easy way to deploy a secondary tier of data storage that can comprise multiple, networked data storage technologies running on diverse operating systems, where data that no longer needs to be in primary storage is protected, classified according to captured metadata,...
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.
License
The LabKey Software Foundation licenses LabKey Server and its documentation for free under the Apache LicenseApache License
The Apache License is a copyfree free software license authored by the Apache Software Foundation . The Apache License requires preservation of the copyright notice and disclaimer....
.
Languages and extensibility
The base platform is written in JavaJava (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...
. It can be extended through the addition of Java-based modules or simple, file-based modules written in HTML
HTML
HyperText Markup Language is the predominant markup language for web pages. HTML elements are the basic building-blocks of webpages....
, XML
XML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
and JavaScript
JavaScript
JavaScript is a prototype-based scripting language that is dynamic, weakly typed and has first-class functions. It is a multi-paradigm language, supporting object-oriented, imperative, and functional programming styles....
. The platform can also be extended using LabKey Server's Java, JavaScript
JavaScript
JavaScript is a prototype-based scripting language that is dynamic, weakly typed and has first-class functions. It is a multi-paradigm language, supporting object-oriented, imperative, and functional programming styles....
, R
R (programming language)
R is a programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software, and R is widely used for statistical software development and data analysis....
, Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
, Perl
Perl
Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions and become widely popular...
and SAS client libraries.
History
LabKey Server was spun out of the Computational Proteomics Lab at the Fred Hutchinson Cancer Research CenterFred Hutchinson Cancer Research Center
The Fred Hutchinson Cancer Research Center, is one of the world’s leading cancer research institutes...
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).
Features
LabKey Server provides a secure data repository for all types of biomedical data, including mass spectrometry, flow cytometryFlow cytometry
Flow cytometry is a technique for counting and examining microscopic particles, such as cells and chromosomes, by suspending them in a stream of fluid and passing them by an electronic detection apparatus. It allows simultaneous multiparametric analysis of the physical and/or chemical...
, microarray
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
, microplate, ELISpot
ELISPOT
The Enzyme-linked immunosorbent spot assay is a common method for monitoring immune responses in humans and animals. It was developed by Cecil Czerkinsky in 1983....
, ELISA
ELISA
Enzyme-linked immunosorbent assay , is a popular format of a "wet-lab" type analytic biochemistry assay that uses one sub-type of heterogeneous, solid-phase enzyme immunoassay to detect the presence of a substance in a liquid sample."Wet lab" analytic biochemistry assays involves detection of an...
, NAb
Neutralizing antibody
A Neutralizing antibody, or NAb is an antibody which defends a cell from an antigen or infectious body by inhibiting or neutralizing any effect it has biologically...
and observational study
Observational study
In epidemiology and statistics, an observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator...
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 PipelineTrans-Proteomic PipelineThe Trans-Proteomic Pipeline is a widely-used freely available open source proteomics data analysis pipeline developed at the Institute for Systems Biology by the Ruedi Aebersold group under the Seattle Proteome Center...
, MascotMascot (software)Mascot is a software search engine that uses mass spectrometry data to identify proteins from primary sequence databases.Many research facilities utilize Mascot, either by private or public server for database searching....
and SequestSEQUESTSEQUEST is a tandem mass spectrometry data analysis program used for protein identification. Sequest identifies collections of tandem mass spectra to peptide sequences that have been generated from databases of protein sequences.-Applications:...
. Certified as "Silver-Level Compliant Data Service" with the caBIGCaBIGThe cancer Biomedical Informatics Grid is an open source, open access information network with the mission of enabling secure data exchange throughout the cancer community...
standard. - Flow Cytometry. Supports automated quality control, centralized data management and web-based data sharing. Integrates with FlowJoFlowJoFlowJo is a software package for analyzing flow cytometry data. Files produced by modern flow cytometers are written in the format with an .fcs file extension...
.
Users
Users range from individual labs to large research consortia. Current users include:- Fred Hutchinson Cancer Research Center
- Statistical Center for HIV/AIDS Research and Prevention (SCHARP)
- Center for HIV-AIDS Vaccine Immunology (CHAVI) at Duke UniversityDuke UniversityDuke University is a private research university located in Durham, North Carolina, United States. Founded by Methodists and Quakers in the present day town of Trinity in 1838, the school moved to Durham in 1892. In 1924, tobacco industrialist James B...
- Collaboration for AIDS Vaccine Discovery (CAVD), funded by the Gates Foundation
- Wisconsin National Primate Research CenterNational Primate Research CenterNational Primate Research Centers are a network of eight research programs in the United States funded by the National Institutes of Health to conduct biomedical research on primates...
- International AIDS Vaccine Initiative (IAVI)
- Infectious Disease Research Institute (IDRI)
- Cedars-Sinai Medical CenterCedars-Sinai Medical CenterOriginally established as Kaspare Cohn Hospital in 1902, Cedars-Sinai Medical Center is a non-profit, tertiary 958-bed hospital and multi-specialty academic health science centre located in Los Angeles, California, US. Part of the Cedars-Sinai Health System, the hospital employs a staff of over...
- Harvard PartnersPartners Harvard Medical InternationalPartners Harvard Medical International is a not-for-profit organization that provides advisory services and professional consulting to organizations outside the United States. PHMI is a subsidiary of Partners HealthCare System, a health care system based in Boston, Massachusetts.-History:PHMI was...
- University of WashingtonUniversity of WashingtonUniversity of Washington is a public research university, founded in 1861 in Seattle, Washington, United States. The UW is the largest university in the Northwest and the oldest public university on the West Coast. The university has three campuses, with its largest campus in the University...
- University of MichiganUniversity of MichiganThe University of Michigan is a public research university located in Ann Arbor, Michigan in the United States. It is the state's oldest university and the flagship campus of the University of Michigan...
- University of KentuckyUniversity of KentuckyThe University of Kentucky, also known as UK, is a public co-educational university and is one of the state's two land-grant universities, located in Lexington, Kentucky...
- University of Wisconsin
- Institute of Molecular and Cell Biology (Singapore)Institute of Molecular and Cell Biology (Singapore)The Institute of Molecular and Cell Biology is an autonomous research institute of the Agency for Science, Technology and Research in Singapore...
External links
- 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.
- SCHARP
- CHAVI
- CAVD
- IAVI
- IDRI