Difference between revisions of "OpenBIS"
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==Product history== | ==Product history== | ||
The earliest known development version of openBIS is v0.14 from December 6, 2007<ref name="BISStart1" />, though earlier work on the system may have been developed "with a privately held biopharmaceutical company."<ref name="AboutBISPDF" /> Development was headed by ETH Zurich in collaboration with the Biozentrum of the University of Basel, the Swiss Institute of Bioinformatics, as well as other academic groups in Switzerland and Europe.<ref name="AboutBISPDF" /> The first public release of openBIS occurred in late-April 2008 as v8.04.<ref name="BISPub1">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=19597255 |title=Download Page - 7 May 2008 |author=Basil, Neff |publisher=Department of Biosystems Science and Engineering - ETHZ |date=7 May 2008 |accessdate=26 September 2012}}</ref> By January 2009 the team had patched the public release to version 8.04.5.<ref name="BISPub2">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=29295838 |title=Download Page - 16 January 2009 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=16 January 2009 |accessdate=26 September 2012}}</ref> On April 21, 2010, the development team announced after 8.04.5 the software would be "completely rewritten to be a flexible framework rather than a system with fixed functionality."<ref name="BISPub3">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=43131420 |title=Download Page - 21 April 2010 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=21 April 2010 |accessdate=26 September 2012}}</ref> As of January 14, 2012, the 8.04.5 public version remains deprecated, and a series of "sprint releases" occur on the development version.<ref name="BISPub4">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=11109400 |title=Download Page - 14 January 2012 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=14 January 2012 |accessdate=26 September 2012}}</ref> The latest development snapshot is | The earliest known development version of openBIS is v0.14 from December 6, 2007<ref name="BISStart1" />, though earlier work on the system may have been developed "with a privately held biopharmaceutical company."<ref name="AboutBISPDF" /> Development was headed by ETH Zurich in collaboration with the Biozentrum of the University of Basel, the Swiss Institute of Bioinformatics, as well as other academic groups in Switzerland and Europe.<ref name="AboutBISPDF" /> The first public release of openBIS occurred in late-April 2008 as v8.04.<ref name="BISPub1">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=19597255 |title=Download Page - 7 May 2008 |author=Basil, Neff |publisher=Department of Biosystems Science and Engineering - ETHZ |date=7 May 2008 |accessdate=26 September 2012}}</ref> By January 2009 the team had patched the public release to version 8.04.5.<ref name="BISPub2">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=29295838 |title=Download Page - 16 January 2009 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=16 January 2009 |accessdate=26 September 2012}}</ref> On April 21, 2010, the development team announced after 8.04.5 the software would be "completely rewritten to be a flexible framework rather than a system with fixed functionality."<ref name="BISPub3">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=43131420 |title=Download Page - 21 April 2010 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=21 April 2010 |accessdate=26 September 2012}}</ref> As of January 14, 2012, the 8.04.5 public version remains deprecated, and a series of "sprint releases" occur on the development version.<ref name="BISPub4">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=11109400 |title=Download Page - 14 January 2012 |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=14 January 2012 |accessdate=26 September 2012}}</ref> The latest development snapshot is S149, released January 31, 2013.<ref name="BISChangeLog">{{cite web |url=https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log |title=openBIS Change Log |publisher=Department of Biosystems Science and Engineering - ETHZ |date=17 September 2012 |accessdate=26 September 2012}}</ref> | ||
==Features== | ==Features== | ||
Revision as of 19:22, 1 February 2013
 | |
| Developer(s) | Center for Information Science and Databases - ETHZ |
|---|---|
| Initial release | December 6, 2007 (v0.14)[1] |
| Stable release |
20.10.7.3 (November 23, 2023) [±] |
| Preview release | S275 (April 25, 2018) [±] |
| Written in | Java[2] |
| Operating system | Linux or Mac OS X |
| Type | Laboratory informatics software |
| License(s) | Apache Software License v2.0[3] |
| Website | http://www.cisd.ethz.ch/ |
openBIS is a free extensible open-source biological information management system designed "to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata." [4]
Product history
The earliest known development version of openBIS is v0.14 from December 6, 2007[1], though earlier work on the system may have been developed "with a privately held biopharmaceutical company."[2] Development was headed by ETH Zurich in collaboration with the Biozentrum of the University of Basel, the Swiss Institute of Bioinformatics, as well as other academic groups in Switzerland and Europe.[2] The first public release of openBIS occurred in late-April 2008 as v8.04.[5] By January 2009 the team had patched the public release to version 8.04.5.[6] On April 21, 2010, the development team announced after 8.04.5 the software would be "completely rewritten to be a flexible framework rather than a system with fixed functionality."[7] As of January 14, 2012, the 8.04.5 public version remains deprecated, and a series of "sprint releases" occur on the development version.[8] The latest development snapshot is S149, released January 31, 2013.[9]
Features
Features include[4]:
- high content screening
- dataset management
- data filter and export
- data integration through API
- distributed storage support
- proteomics-based functionality
- metabolomics-based functionality
- Illumina NGS data management
Hardware/software requirements
Current requirements include[10]:
- Linux or Mac OS X operating system
- PostgreSQL 9.0 or higher (with database superuser privileges)
- Java 1.5 or higher
Videos, screenshots, and other media
Numerous videos for openBIS can be found on the openBIS website.
Entities using openBIS
According to the developers, openBIS is used by[2]:
- research projects of SystemsX.ch
- research consortia funded by the European Union
Further reading
- Bauch, Angela; Adamczyk, Izabela; Buczek, Piotr; Elmer, Franz-Josef; Enimanev, Kaloyan; Glyzewski, Pawel; Kohler, Manuel; Pylak, Tomasz; Quandt, Andreas; Ramakrishnan, Chandrasekhar; Beisel, Christian; Malmström, Lars; Aebersold, Ruedi; Rinn, Bernd (2011). "openBIS: a flexible framework for managing and analyzing complex data in biology research". BMC Bioinformatics 12: 468. doi:10.1186/1471-2105-12-468. http://www.biomedcentral.com/1471-2105/12/468.
External links
References
- ↑ 1.0 1.1 Bernd, Rinn (11 December 2007). "Download Page". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=11110898. Retrieved 26 September 2012.
- ↑ 2.0 2.1 2.2 2.3 "openBIS - Biology Information System" (PDF). Department of Biosystems Science and Engineering - ETHZ. https://wiki.systemsx.ch/download/attachments/37390198/openBIS_HCS.pdf. Retrieved 26 September 2012.
- ↑ Bernd, Rinn (11 December 2007). "Copying - openBIS". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/display/bis/Copying. Retrieved 26 September 2012.
- ↑ 4.0 4.1 "openBIS". Center for Information Science and Databases - ETHZ. 25 January 2011. http://www.cisd.ethz.ch/software/openBIS. Retrieved 26 September 2012.
- ↑ Basil, Neff (7 May 2008). "Download Page - 7 May 2008". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=19597255. Retrieved 26 September 2012.
- ↑ Bernd, Rinn (16 January 2009). "Download Page - 16 January 2009". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=29295838. Retrieved 26 September 2012.
- ↑ Bernd, Rinn (21 April 2010). "Download Page - 21 April 2010". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=43131420. Retrieved 26 September 2012.
- ↑ Bernd, Rinn (14 January 2012). "Download Page - 14 January 2012". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=11109400. Retrieved 26 September 2012.
- ↑ "openBIS Change Log". Department of Biosystems Science and Engineering - ETHZ. 17 September 2012. https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log. Retrieved 26 September 2012.
- ↑ "openBIS Setup Guide". Center for Information Science and Databases - ETHZ. 17 September 2012. https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+setup+guide#openBISsetupguide-Prerequisites. Retrieved 26 September 2012.
