Difference between revisions of "OpenBIS"

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{{lowercase title}}
{{Infobox software
| name                  = openBIS
| title                  = openBIS
| logo                  = [[Image:OpenBIS_Logo_white_bg.png‎|140px]]
| screenshot            = <!-- [[File: ]] -->
| caption                =
| collapsible            =
| author                =
| developer              = Center for Information Science and Databases - ETHZ
| released              = {{Start date|2007|12|06}} (v0.14)<ref name="BISStart1">{{cite web |url=https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=11110898 |title=Download Page |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=11 December 2007 |accessdate=26 September 2012}}</ref>
| discontinued          =
| frequently updated    = yes<!-- Release version update? Don't edit this page, just click on the version number! -->
| programming language  = Java<ref name="AboutBISPDF">{{cite web |url=https://wiki.systemsx.ch/download/attachments/37390198/openBIS_HCS.pdf |format=PDF |title=openBIS - Biology Information System |publisher=Department of Biosystems Science and Engineering - ETHZ |accessdate=26 September 2012}}</ref>
| operating system      = Linux or Mac OS X
| platform              =
| size                  =
| language              =
| status                =
| genre                  = [[Laboratory informatics]] software
| license                = Apache Software License v2.0<ref name="BISCopy">{{cite web |url=https://wiki-bsse.ethz.ch/display/bis/Copying |title=Copying - openBIS |author=Bernd, Rinn |publisher=Department of Biosystems Science and Engineering - ETHZ |date=11 December 2007 |accessdate=26 September 2012}}</ref>
| website                = [http://www.cisd.ethz.ch/software/openBIS 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." <ref name="BISHome">{{cite web |url=http://www.cisd.ethz.ch/software/openBIS |title=openBIS |publisher=Center for Information Science and Databases - ETHZ |date=25 January 2011 |accessdate=26 September 2012}}</ref>
==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>
On April 4, 2013, the long series of "sprint releases" of the development version culminated in an official new production release as version 13.04.<ref name="BISPub4">{{cite web |url=https://wiki-bsse.ethz.ch/pages/diffpages.action?originalId=96536728&pageId=96536730 |title=Download Page - 04 April 2013 |author=Chandrasekhar, Ramakrishnan |publisher=Department of Biosystems Science and Engineering - ETHZ |date=04 April 2013 |accessdate=23 April 2013}}</ref> Development on the software continues with the orginal pattern of sprint releases, with the latest development snapshot S219 appearing December 11, 2015.<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=20 December 2013 |accessdate=06 January 2016}}</ref>
In late September 2014, the openBIS team revealed an [[electronic laboratory notebook]] plug-in that could be added that would add functionality like managing inventory, uploading data sets, managing experiments, and automate the creation of spaces, projects, and experiments in the system.<ref name="oBELN">{{cite web |url=https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+ELN |title=openBIS for ELN |author=CISD Documentation Administrator |publisher=Department of Biosystems Science and Engineering - ETHZ |date=26 September 2014 |accessdate=07 October 2014}}</ref>
==Features==
Features include<ref name="BISHome" /><ref name="oBELN" />:
* 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
* ELN functionality via a separate plug-in
==Hardware/software requirements==
Current requirements include<ref name="BISSetupGuide">{{cite web |url=https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+setup+guide#openBISsetupguide-Prerequisites |title=openBIS Setup Guide |publisher=Center for Information Science and Databases - ETHZ |date=17 September 2012 |accessdate=26 September 2012}}</ref>:
* 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 [https://wiki-bsse.ethz.ch/display/bis/openBIS+Screen+Casts openBIS website].
Instructions for installing the ELN plug-in can be found [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+ELN here].
==Entities using openBIS==
According to the developers, openBIS is used by<ref name="AboutBISPDF" />:
* research projects of [http://www.systemsx.ch/ SystemsX.ch]
* research consortia funded by the European Union
==Further reading==
* {{cite journal |journal=BMC Bioinformatics |title=openBIS: a flexible framework for managing and analyzing complex data in biology research |author=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  |volume=12 |pages=468 |year=2011 |doi=10.1186/1471-2105-12-468 |pmid=22151573 |pmc=PMC3275639}}
==External links==
* [https://wiki-bsse.ethz.ch/display/bis/Home openBIS wiki]
* [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS openBIS documentation]
* [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+setup+guide openBIS setup guide]
==References==
<references />
<!---Place all category tags here-->
[[Category:Bioinformatics software (open source)]]
[[Category:Electronic laboratory notebooks (open source)]]
[[Category:Laboratory informatics software (open source)]]
[[Category:Laboratory information management systems (open source)]]

Revision as of 17:38, 12 February 2016

openBIS
OpenBIS Logo white bg.png
Developer(s) Center for Information Science and Databases - ETHZ
Initial release December 6, 2007 (2007-12-06) (v0.14)[1]
Stable release

20.10.7.3  (November 23, 2023; 5 months ago (2023-11-23))

[±]
Preview release S275  (April 25, 2018; 6 years ago (2018-04-25)) [±]
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]

On April 4, 2013, the long series of "sprint releases" of the development version culminated in an official new production release as version 13.04.[8] Development on the software continues with the orginal pattern of sprint releases, with the latest development snapshot S219 appearing December 11, 2015.[9]

In late September 2014, the openBIS team revealed an electronic laboratory notebook plug-in that could be added that would add functionality like managing inventory, uploading data sets, managing experiments, and automate the creation of spaces, projects, and experiments in the system.[10]

Features

Features include[4][10]:

  • 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
  • ELN functionality via a separate plug-in

Hardware/software requirements

Current requirements include[11]:

  • 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.

Instructions for installing the ELN plug-in can be found here.

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


External links

References

  1. ↑ 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. ↑ 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. 
  3. ↑ 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. ↑ 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. 
  5. ↑ 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. 
  6. ↑ 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. 
  7. ↑ 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. 
  8. ↑ Chandrasekhar, Ramakrishnan (4 April 2013). "Download Page - 04 April 2013". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/pages/diffpages.action?originalId=96536728&pageId=96536730. Retrieved 23 April 2013. 
  9. ↑ "openBIS Change Log". Department of Biosystems Science and Engineering - ETHZ. 20 December 2013. https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log. Retrieved 06 January 2016. 
  10. ↑ 10.0 10.1 CISD Documentation Administrator (26 September 2014). "openBIS for ELN". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+for+ELN. Retrieved 07 October 2014. 
  11. ↑ "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. 
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