Difference between revisions of "LabKey Server"
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==Features== | ==Features== | ||
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 to biomedical research. | LabKey Server provides a secure data repository for all types of biomedical data, including [[mass spectrometry]], [[flow cytometry]], microarray, [[Microtiter plate|microplate]], ELISpot, ELISA, NAb, and observational study information. A customizable data processing pipeline allows the upload and processing of the large data files common to biomedical research. | ||
The platform also provides domain-specific support for several areas of research, including: | The platform also provides domain-specific support for several areas of research, including: | ||
Revision as of 01:54, 21 April 2012
| Developer(s) | LabKey Corporation and the LabKey Software Foundation |
|---|---|
| Initial release | April 16, 2007[1] |
| Stable release |
24.3.0 (March 25, 2024) [±] |
| Preview release | 20.11 [±] |
| Written in | Java |
| Operating system | Cross-platform |
| Type | Laboratory informatics software |
| License(s) | Apache Software License[2] |
| Website | LabKey.org |
LabKey Server is a free open-source laboratory informatics solution released under an Apache license. LabKey acts primarily as a web-based data management platform, though through its use of application programming interfaces (APIs), the software remains highly extensible. LabKey has been adapted to a variety of disciplines, including proteomics, flow cytometry, and observational study management.[3]
LabKey Corporation, the company the develops the software, also sells a number of professional services, including installations and upgrade assistance, training programs, customization, consulting, and support.[4]
Product history
The origins of LabKey Server trace back to 2003, where at the Fred Hutchinson Cancer Research Center (FHCRC) (located in Seattle, Washington) Professor Martin McIntosh saw a need for robust software that would facilitate cooperative proteomics and cancer research, with projects such as the Human Genome Project and the National Cancer Institute's (NCI's) caBIG as inspiration.[5][6] By October 2003, McIntosh had recruited three former Microsoft programmers — Mark Igra, Matthew Bellew, and Adam Rauch — to begin development on the core of an open-source application that would later be called the Computational Portal and Analysis System or CPAS.[7][6][8] Initial development was funded by the NCI and the nonprofit organization Canary Foundation.[5][9]
As early beta versions of the program floated around the Research Center, popularity grew, necessitating more resources. With the help of the FHCRC, Janaury 2005 saw the creation of a new entity called LabKey Software to better focus on the development of the software and to better support other institutions that would go on to utilize it. Additionally, another cohort of three former Microsoft developers joined the team to aid with development: George Snelling, Peter Hussey and Brendan MacLean.[6][8] The first public release of the software came on November 23, 2005, in the form of CPAS 1.1.[7][1] A few weeks later the team released the source code to coincide with the the January 1, 2006 print publication of the groups corresponding paper in the Journal of Proteome Research, making it officially an open-source release.[10] At that time, key features of the application included multiple standard-file formats, protein database search functionality, comprehensive experiment annotation, data sharing, and several proteomic-friendly analytic tools.[11]
Over the next year CPAS went through several iterations, including an update to a more specific name of Computational Proteomics Analysis System. The software held the name up to version 1.7, released in December 2006. With version 2.0, released on April 16, 2007, came a renaming of the product to what is still known today as LabKey Server.[1][9][12] In May 2007, the Canary Foundation announced the fifteen grant recipients of their $225,000 Bioinformatics Platform Dissemination Award, all of which would go towards the future design, development, and support of LabKey's software.[13] That set of grant funding brought new features to CPAS/LabKey Server, including: improved label-free comparisons; MS peptide intensity data modules; and a more central integration of MsInspect, the signal processing component for locating and quantitating peptides.[14]
The 2.x incrementation ended with version 2.3 in February 2008.[1] The subsequent release after version 2.3 was 8.1 on May 1, 2008, though the increment jump was never publicly explained.[15]
Shortly after release of 8.1, several news releases indicated LabKey would be lending support to Seattle businesses Insilicos and the Institute for Systems Biology (ISB). The goal of the collaboration was to port proteomics software tools like LabKey Server through Amazon's cloud servers, allowing potential research groups with IT budgets to utilize the proteomics applications and scale up web service as demand grows.[16][17] A few months later, LabKey announced another collaboration, this time with the Microsoft BioIT Alliance, an association of life science organizations and informatics companies focused on accelerating the pace of drug discovery and development.[18]
Version 9.1 of LabKey was released on April 2, 2009[19], with 10.1 arriving in March 2010[20] and 11.1 releasing in April 2011.[21] The latest version, 11.3, went live in December 2011, featuring enhanced data management, data visualization, and security functions.
Features
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 to 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
- data repository: manages biomedical data, including raw data sets and spreadsheets; handles the data from built-in collaboration tools like the wiki and message board
Hardware/software requirements
Components necessary for a Windows installation of LabKey Server are included in the binary Windows Installer. More complex installations may need to be done manually, which will require the separate installation of components.
For all details concerning manual and automatic installation (and any necessary requirements), please consult the Before You Install page of the software documentation.
Videos, screenshots, and other media
Videos
The following demonstration videos are available for LabKey Server:
- Visualize group data trends
- Ancillary studies
- Data browser
- LabKey at the Cascadia Proteomics Symposium
- Time charts: Comparing multiple measures on one chart
- Specimens: Tracking participant consent
- Security: Study demonstration mode
- Delivering diagnostic results
- Unlocking spreadsheet data #1: The problem
- Unlocking spreadsheet data #2: Projects and sample sets
- Unlocking spreadsheet data #3: Upload and search files
- Unlocking spreadsheet data #4: Import assay results
- Unlocking spreadsheet data #5: Integrate and analyze
- 11.3 Video Demonstrations: New User Interface Features
- 11.3 Video Demonstrations: Visualizing Group Data Trends
- 11.3 Video Demonstrations: Ancillary Studies
Screenshots
The following screenshots are available for LabKey Server:
Demos and live examples
Entities using LabKey Server
Examples of entities using LabKey Server include:
AdaptiveTCR, Bill & Melinda Gates Foundation, Fred Hutchinson Cancer Research Center, Harvard Partners, Institute of Molecular and Cell Biology – Singapore, Katze Lab at University of Washington, National Institute of Allergy and Infectious Diseases at Duke University, Stanford Canary Center for Cancer Early Detection, Statistical Center for HIV/AIDS Research & Prevention, USC Center for Applied Molecular Medicine
Source: The Showcase of Live Sites, LabKey CPAS Overview, and Our Clients pages
See also
Further reading
- "LabKey Server documentation". LabKey Software Foundation. https://www.labkey.org/project/home/Documentation/begin.view?.
- Rauch, A.; M. Bellew; J. Eng; M. Fitzgibbon; T. Holzman; P. Hussey; M. Igra; B. Maclean; C. W. Lin; A. Detter; R. Fang; V. Faca; P. Gafken; H. Zhang; J. Whiteaker; D. States; S. Hanash; A. Paulovich; M. W. McIntosh (January 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. PMID 16396501. http://www.ncbi.nlm.nih.gov/pubmed/16396501.
- Nelson, Elizabeth K.; Britt Piehler; Josh Eckels; Adam Rauch; Matthew Bellew; Peter Hussey; Sarah Ramsay; Cory Nathe; Karl Lum; Kevin Krouse; David Stearns; Brian Connolly; Tom Skillman; Mark Igra (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. http://www.biomedcentral.com/1471-2105/12/71.
External links
- LabKey corporate site
- LabKey Server at Freecode
- LabKey Server and CPAS archived documentation
- LabKey Server and CPAS archived news
References
- ↑ 1.0 1.1 1.2 1.3 "LabKey Software Foundation - News". LabKey Software Foundation. https://www.labkey.org/announcements/home/begin.view. Retrieved 20 April 2012.
- ↑ "LabKey Frequently Asked Questions". LabKey Software Foundation. https://www.labkey.org/wiki/home/page.view?name=HomeFAQ. Retrieved 20 April 2012.
- ↑ "LabKey Server". LabKey Corporation. http://labkey.com/server/labkey-server. Retrieved 20 April 2012.
- ↑
- ↑ 5.0 5.1 "Center, NCI launch open-source software for proteomics analysis". Fred Hutchinson Cancer Research Center. 5 January 2006. http://www.fhcrc.org/content/public/en/news/center-news/2006/01/proteomics-software.html. Retrieved 20 April 2012.
- ↑ 6.0 6.1 6.2 Nelson, Elizabeth (2 January 2011). "A Seattle Version of the Silicon Valley Garage". LabKey Corporation. http://labkey.com/blog/2011/01/tools-%E2%80%B9-labkey-blog-%E2%80%94-wordpress. Retrieved 20 April 2012.
- ↑ 7.0 7.1 "CPAS - Computational Portal and Analysis System". Fred Hutchinson Cancer Research Center. 23 November 2005. Archived from the original on 24 November 2005. http://web.archive.org/web/20051124131402/http://cpas.fhcrc.org/Project/home/home.view. Retrieved 20 April 2012.
- ↑ 8.0 8.1 Berg, Barbara (17 March 2005). "'Wizards' of computational science". Fred Hutchinson Cancer Research Center. http://www.fhcrc.org/content/public/en/news/center-news/2005/03/wizards-computational-science.html. Retrieved 20 April 2012.
- ↑ 9.0 9.1 "LabKey CPAS Overview". LabKey Software Foundation. https://www.labkey.org/Project/home/CPAS/begin.view. Retrieved 20 April 2012.
- ↑ Snelling, George (8 December 2005). "CPAS 1.1 Source Code Released". LabKey Software Foundation. https://www.labkey.org/announcements/home/thread.view?rowId=35. Retrieved 20 April 2012.
- ↑ "Hutchinson Center and NCI launch open-source software for proteomics analysis" (DOC). Fred Hutchinson Cancer Research Center. 8 December 2005. http://proteomics.fhcrc.org/CPL/_docs/CPAS_media_backgrounder.doc. Retrieved 20 April 2012.
- ↑ "Computational Proteomics Laboratory". Fred Hutchinson Cancer Research Center. http://proteomics.fhcrc.org/CPL/home.html. Retrieved 20 April 2012.
- ↑ "Grant Awardees Standardize Software Platform for Early Cancer Detection". Canary Foundation. 22 May 2007. http://www.canaryfoundation.org/newsroom/press-releases/grant-awardees-standardize-software-platform-for-early-cancer-detection/. Retrieved 20 April 2012.
- ↑ "CPAS update". International Cancer Biomarker Consortium Newsletter (Fred Hutchinson Cancer Research Center) 3 (4). December 2007. http://cairob.fhcrc.org/science/international_biomarker/news/2007/december.html. Retrieved 20 April 2012.
- ↑ "Get Started With LabKey Server 8.1". LabKey Software Foundation. 1 May 2008. https://www.labkey.org/project/home/Documentation/Archive/8.1/begin.view?. Retrieved 20 April 2012.
- ↑ "Insilicos Awarded Grant for Life Science Computing". Insilicos LLC. 5 May 2008. http://insilicos.com/news/insilicos-awarded-grant-for-life-science-computing. Retrieved 20 April 2012.
- ↑ Toner, Bernadette (9 May 2008). "Insilicos Partners with LabKey, ISB to Port Proteomics Software Tools to Amazon’s Cloud". Genomeweb LLC. http://www.genomeweb.com/informatics/insilicos-partners-labkey-isb-port-proteomics-software-tools-amazon’s-cloud. Retrieved 20 April 2012.
- ↑ "LabKey Software Joins BioIT Alliance". Business Wire. 18 September 2012. http://www.businesswire.com/news/google/20080918005145/en. Retrieved 20 April 2012.
- ↑ "Get Started With LabKey Server 9.1". LabKey Software Foundation. 2 April 2009. https://www.labkey.org/project/home/Documentation/Archive/9.1/begin.view?. Retrieved 20 April 2012.
- ↑ "Get Started With LabKey Server 10.1". LabKey Software Foundation. 10 March 2010. https://www.labkey.org/project/home/Documentation/Archive/10.1/begin.view?. Retrieved 20 April 2012.
- ↑ "Get Started With LabKey Server v11.1". LabKey Software Foundation. 12 April 2011. https://www.labkey.org/project/home/Documentation/Archive/11.1/begin.view?. Retrieved 20 April 2012.
