LabKey Server is a software suite available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure

data repository A data library, data archive, or data repository is a collection of numeric and/or geospatial data sets for secondary use in research. A data library is normally part of a larger institution (academic, corporate, scientific, medical, government ...

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 Pipeline may refer to: Electronics, computers and computing * Pipeline (computing), a chain of data-processing stages or a CPU optimization found on ** Instruction pipelining, a technique for implementing instruction-level parallelism within a s ...

License

LabKey licenses LabKey Server and its documentation for free under the Apache License.

Languages and extensibility

The base platform is written in

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...

. It can be extended through the addition of Java-based modules or simple, file-based modules written in

HTML The HyperText Markup Language or HTML is the standard markup language for documents designed to be displayed in a web browser. It can be assisted by technologies such as Cascading Style Sheets (CSS) and scripting languages such as JavaScri ...

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. ...

and

JavaScript JavaScript (), often abbreviated as JS, is a programming language that is one of the core technologies of the World Wide Web, alongside HTML and CSS. As of 2022, 98% of Website, websites use JavaScript on the Client (computing), client side ...

. The platform can also be extended using LabKey Server's

, R, Python,

Perl Perl is a family of two High-level programming language, high-level, General-purpose programming language, general-purpose, Interpreter (computing), interpreted, dynamic programming languages. "Perl" refers to Perl 5, but from 2000 to 2019 it ...

and SAS client libraries.

History

LabKey Server, originally known as the Computational Proteomics Analysis System (CPAS), was developed at the

Fred Hutchinson Cancer Research Center The Fred Hutchinson Cancer Center, formerly known as the Fred Hutchinson Cancer Research Center and also known as Fred Hutch or The Hutch, is a cancer research institute established in 1975 in Seattle, Washington. History The center grew out ...

to manage high volumes of data generated at the Fred Hutch Computational Proteomics Lab. In 2005, a small team spun out of the Hutch and began operating independently as LabKey Software after contributors realized that the software could be beneficial to the broader scientific community.

Core Components

LabKey Server provides a secure data repository for all types of biomedical data, including mass spectrometry,

flow cytometry Flow cytometry (FC) is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles. In this process, a sample containing cells or particles is suspended in a fluid and injected into the fl ...

microarray A microarray is a multiplex lab-on-a-chip. Its purpose is to simultaneously detect the expression of thousands of genes from a sample (e.g. from a tissue). It is a two-dimensional array on a solid substrate—usually a glass slide or silic ...

microplate A microplate, also known as a microtiter plate (''Microtiter'' is a registered trademark in the United States, therefore it should not be used generically without attribution), microwell plate or multiwell, is a flat plate with multiple "wells" ...

ELISpot The enzyme-linked immune absorbent spot (ELISpot) is a type of assay that focuses on quantitatively measuring the frequency of cytokine secretion for a single cell. The ELISpot Assay is also a form of immunostaining since it is classified as a tec ...

ELISA The enzyme-linked immunosorbent assay (ELISA) (, ) is a commonly used analytical biochemistry assay, first described by Eva Engvall and Peter Perlmann in 1971. The assay uses a solid-phase type of enzyme immunoassay (EIA) to detect the presence ...

, NAb and

observational study In fields such as epidemiology, social sciences, psychology and statistics, an observational study draws inferences from a sample to a population where the independent variable is not under the control of the researcher because of ethical co ...

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 Longitudinal is a geometric term of location which may refer to: * Longitude ** Line of longitude, also called a meridian * Longitudinal engine, an internal combustion engine in which the crankshaft is oriented along the long axis of the vehicle, ...

, 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 The Trans-Proteomic Pipeline (TPP) is an open-source data analysis software for proteomics developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold group under the Seattle Proteome Center. The TPP includes PeptideProphet, Pr ...

Mascot A mascot is any human, animal, or object thought to bring luck, or anything used to represent a group with a common public identity, such as a school, professional sports team, society, military unit, or brand name. Mascots are also used as fic ...

and Sequest. Certified as "Silver-Level Compliant Data Service" with the

caBIG The cancer Biomedical Informatics Grid (caBIG) was a US government program to develop an open-source, open access information network called caGrid for secure data exchange on cancer research. The initiative was developed by the National Cance ...

standard. * Flow Cytometry. Supports automated quality control, centralized data management and web-based data sharing. Integrates with FlowJo.

Zika Open Research Portal

In 2016, LabKey and Professor Dave O'Connor of the

University of Wisconsin–Madison A university () is an institution of higher (or tertiary) education and research which awards academic degrees in several academic disciplines. ''University'' is derived from the Latin phrase ''universitas magistrorum et scholarium'', which ...

launched the Zika Open Research Porta

using LabKey Server. The portal provides direct access to experiment data being produced by members of the Zika Experimental Science Team (ZEST). The portal received attention from the scientific community for being the first platform of its kind to share real-time research data.

Open Source Software

Labkey is licensed in a variety of manners. Source-code is provided for a core set of features with the Community Edition, and there are also Premium Editions available.

Users

Users range from individual labs to large research consortia. In 2017, the program's users included the following: *

Cedars-Sinai Medical Center Cedars-Sinai Medical Center is a nonprofit, tertiary, 886-bed teaching hospital and multi-specialty academic health science center located in Los Angeles, California. Part of the Cedars-Sinai Health System, the hospital employs a staff of over 2, ...

* Center for HIV-AIDS Vaccine Immunology (CHAVI) at Duke University * Collaboration for AIDS Vaccine Discovery (CAVD), funded by the

Gates Foundation The Bill & Melinda Gates Foundation (BMGF), a merging of the William H. Gates Foundation and the Gates Learning Foundation, is an American private foundation founded by Bill Gates and Melinda French Gates. Based in Seattle, Washington, it was ...

* Fred Hutchinson Cancer Research Center *

Genomics England Genomics England is a British company set up and owned by the United Kingdom Department of Health and Social Care to run the 100,000 Genomes Project. The project aimed in 2014 to sequence 100,000 genomes from NHS patients with a rare disease an ...

* International AIDS Vaccine Initiative (IAVI) * Infectious Disease Research Institute (IDRI) *

Institute of Molecular and Cell Biology (Singapore) The Agency for Science, Technology and Research (A*STAR) is a statutory board under the Ministry of Trade and Industry of Singapore. The agency supports R&D that is aligned to areas of competitive advantage and national needs for Singapore. ...

* Just Biotherapeutics * NIMML * Oregon

National Primate Research Center National Primate Research Centers are a network of seven research programs in the United States funded by the National Institutes of Health to conduct biomedical research on primates. Each center is affiliated with a university or other host institu ...

* Harvard Partners * Statistical Center for HIV/AIDS Research and Prevention (SCHARP) * Southwest

University of Washington The University of Washington (UW, simply Washington, or informally U-Dub) is a public research university in Seattle, Washington. Founded in 1861, Washington is one of the oldest universities on the West Coast; it was established in Seat ...

University of Michigan , mottoeng = "Arts, Knowledge, Truth" , former_names = Catholepistemiad, or University of Michigania (1817–1821) , budget = $10.3 billion (2021) , endowment = $17 billion (2021)As o ...

University of Kentucky The University of Kentucky (UK, UKY, or U of K) is a public land-grant research university in Lexington, Kentucky. Founded in 1865 by John Bryan Bowman as the Agricultural and Mechanical College of Kentucky, the university is one of the state's ...

University of South Florida The University of South Florida (USF) is a public research university with its main campus located in Tampa, Florida, and other campuses in St. Petersburg and Sarasota. It is one of 12 members of the State University System of Florida. USF i ...

University of Wisconsin A university () is an institution of higher (or tertiary) education and research which awards academic degrees in several academic disciplines. ''University'' is derived from the Latin phrase ''universitas magistrorum et scholarium'', which ...

* Tulane

* Wisconsin

Publications

* * * *

References

External links

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