Difference between revisions of "OpenBIS"

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| genre                  = [[Laboratory informatics]] software
| 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>
| 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                = [https://openbis-eln-lims.ethz.ch/ https://openbis-eln-lims.ethz.ch/]
| website                = [https://openbis.ch/ https://openbis.ch/]<br />[https://sis.id.ethz.ch/services/rdm/openbis.html https://sis.id.ethz.ch/services/rdm/openbis.html]
}}
}}


'''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>
'''openBIS''' is a free "open platform for managing scientific information ... [designed] to support research data workflows from bench to publication."<ref name="OBHomeRedirect">{{cite web |url=https://sis.id.ethz.ch/software/openbis.html |title=Data Management Software Platform openBIS |publisher=ETH Zürich |accessdate=23 August 2016}}</ref> The software comes bundled with an [[electronic laboratory notebook]] - [[laboratory information management system]] (ELN-LIMS) plug-in to extend the software's usefulness.<ref name="OBHomeRedirect" />


==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> The software was originally described as 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="BISHomeArch">{{cite web |url=http://www.cisd.ethz.ch/software/openBIS |archiveurl=https://web.archive.org/web/20110212152245/http://www.cisd.ethz.ch/software/openBIS |title=openBIS |publisher=Center for Information Science and Databases - ETHZ |date=25 January 2011 |archivedate=12 February 2011 |accessdate=23 August 2016}}</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>


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 original pattern of sprint releases, every two weeks.<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=02 March 2016}}</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, every two weeks.<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=02 March 2016}}</ref>
In late September 2014, the openBIS team revealed an [[electronic laboratory notebook|ELN]]-[[laboratory information management system|LIMS]] 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><ref name="FuentesSIS14">{{cite web |url=https://wiki.systemsx.ch/download/attachments/91753082/Sybit%20ELN.pdf?version=1&modificationDate=1402649849499&api=v2 |archiveurl=https://web.archive.org/web/20160823153756/https://wiki.systemsx.ch/download/attachments/91753082/Sybit%20ELN.pdf?version=1&modificationDate=1402649849499&api=v2 |title=ELN-LIMS Project |author=Fuentes, J. |pages=15 |publisher=ETH Zürich |date=06 November 2014 |archivedate=23 August 2016 |accessdate=23 August 2016}}</ref>. Work on the plug-in continued throughout 2015 and 2016 in sprint releaes<ref name="BISChangeLogArch1">{{cite web |url=https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log |archiveurl=https://web.archive.org/web/20160823154943/https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log |title=openBIS Change Log |author=CISD Documentation Administrator |publisher=Department of Biosystems Science and Engineering - ETHZ |date=19 August 2016 |archivedate=23 August 2016 |accessdate=23 August 2016}}</ref>
In May 2016 the new major openBIS release 16.05 became available.


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>. The ELN plugin is now included in the openBIS 16.05 installer.
On May 11, 2016 a new major openBIS release became available as version 16.05. A user interface for the ELN-LIMS plug-in was added, and the plug-in was officially integrated into the openBIS 16.05 installer.<ref name="OB1605">{{cite web |url=https://wiki-bsse.ethz.ch/display/openBISDoc1605/openBIS+Change+Log |title=openBIS Change Log - openBIS Documentation Rel. 16.05 |author=Franz-Josef, E. |publisher=Department of Biosystems Science and Engineering - ETHZ |date=18 May 2016 |accessdate=23 August 2016}}</ref>


==Features==
==Features==


Features include<ref name="BISHome" /><ref name="oBELN" />:
openBIS features include<ref name="OBHomeRedirect" />:


* high content screening
* high-content screening data management
* dataset management
* protein identification and quantification data management
* data filter and export
* data integration through API
* distributed storage support
* proteomics-based functionality
* metabolomics-based functionality
* Illumina NGS data management
* Illumina NGS data management
* ELN functionality via a separate plug-in
 
The ELN-LIMS module adds<ref name="OB-ELNLIMSAddon">{{cite web |url=https://sis.id.ethz.ch/software/eln.html |title=openBIS ELN-LIMS for the Life Sciences |publisher=ETH Zürich |accessdate=23 August 2016}}</ref>:
 
* ELN functionality
* sample and SOP management
* sample storage management
* instrument integration
* upload/download of excel-compatible tsv files
* integration with PlasMapper for plasmid maps generation
* integration with BLAST for sequence similarity searches
* data export


==Hardware/software requirements==
==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>:
Current (16.05) requirements include<ref name="BISSetupGuide">{{cite web |url=https://unlimited.ethz.ch/display/openBISDoc2010/openBIS+setup+guide |title=openBIS Setup Guide |publisher=Center for Information Science and Databases - ETHZ |date=12 November 2020 |accessdate=04 May 2021}}</ref>:


* Linux or Mac OS X operating system
* Linux or Mac OS X operating system
* PostgreSQL 9.1 or higher (with database superuser privileges)
* PostgreSQL 11 or higher (with database superuser privileges)
* Java 1.6 or higher
* Java 11 or higher


==Videos, screenshots, and other media==
==Videos, screenshots, and other media==


Numerous videos for openBIS can be found on the [https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=43126125 openBIS website].
Numerous videos for openBIS can be found on the [https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=43126125 openBIS website].
Webinars for the openBIS ELN-LIMS can be found on the [https://openbis-eln-lims.ethz.ch/index.php/webinars/ openBIS ELN-LIMS website].
Instructions for installing the ELN plug-in can be found [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+ELN-LIMS here].


==Entities using openBIS==
==Entities using openBIS==
Line 73: Line 74:


==Further reading==
==Further reading==
 
* {{cite journal |journal=Bioinformatics |title=openBIS ELN-LIMS: An open-source database for academic laboratories |author=Barillari, Caterina; Ottoz, Diana S.M.; Fuentes-Serna, Juan M.; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian |volume=32 |issue=4 |pages=638–640 |year=2016 |doi=10.1093/bioinformatics/btv606 |pmid=26508761 |pmc=PMC4743625}}
* {{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}}
* {{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}}
* {{cite journal |journal=Bioinformatics |title= openBIS ELN-LIMS: an open-source database for academic laboratories. |author=Barillari, Caterina; Ottoz, Diana SM; Fuentes-Serna, Juan M; Rudolf, Fabian; Rinn, Bernd  |volume=32(4) |pages=638 |year=2016 |doi=10.1093/bioinformatics/btv606}}


==External links==
==External links==


* [https://wiki-bsse.ethz.ch/display/bis/Home openBIS wiki]
* [https://sissource.ethz.ch/sispub/openbis openBIS source code]
* [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS openBIS Sprint documentation]
* [https://unlimited.ethz.ch/display/openBISDoc2010/openBIS+Documentation+Rel.+20.10+Home openBIS master documentation]
* [https://wiki-bsse.ethz.ch/display/openBISDoc1605/openBIS openBIS 16.05 release documentation]
* [https://openbis.ch/index.php/docs/user-documentation openBIS user documentation]
* [https://openbis-eln-lims.ethz.ch/ openBIS ELN-LIMS]
* [https://openbis.ch/index.php/docs/admin-documentation/ openBIS admin documentation]
* [https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+setup+guide openBIS setup guide]
* [https://sis.id.ethz.ch/software/openbis.html openBIS site]


==References==
==References==

Latest revision as of 17:22, 27 October 2023

openBIS
OpenBIS Logo white bg.png
Developer(s) Scientific IT Services - ETHZ
Initial release December 6, 2007 (2007-12-06) (v0.14)[1]
Stable release

20.10.7.3  (November 23, 2023; 11 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 https://openbis.ch/
https://sis.id.ethz.ch/services/rdm/openbis.html

openBIS is a free "open platform for managing scientific information ... [designed] to support research data workflows from bench to publication."[4] The software comes bundled with an electronic laboratory notebook - laboratory information management system (ELN-LIMS) plug-in to extend the software's usefulness.[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] The software was originally described as 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." [7]. 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."[8]

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.[9] Development on the software continues with the original pattern of sprint releases, every two weeks.[10]

In late September 2014, the openBIS team revealed an ELN-LIMS 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.[11][12]. Work on the plug-in continued throughout 2015 and 2016 in sprint releaes[13]

On May 11, 2016 a new major openBIS release became available as version 16.05. A user interface for the ELN-LIMS plug-in was added, and the plug-in was officially integrated into the openBIS 16.05 installer.[14]

Features

openBIS features include[4]:

  • high-content screening data management
  • protein identification and quantification data management
  • Illumina NGS data management

The ELN-LIMS module adds[15]:

  • ELN functionality
  • sample and SOP management
  • sample storage management
  • instrument integration
  • upload/download of excel-compatible tsv files
  • integration with PlasMapper for plasmid maps generation
  • integration with BLAST for sequence similarity searches
  • data export

Hardware/software requirements

Current (16.05) requirements include[16]:

  • Linux or Mac OS X operating system
  • PostgreSQL 11 or higher (with database superuser privileges)
  • Java 11 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
  • research groups at ETH

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 4.2 "Data Management Software Platform openBIS". ETH Zürich. https://sis.id.ethz.ch/software/openbis.html. Retrieved 23 August 2016. 
  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. ↑ "openBIS". Center for Information Science and Databases - ETHZ. 25 January 2011. Archived from the original on 12 February 2011. https://web.archive.org/web/20110212152245/http://www.cisd.ethz.ch/software/openBIS. Retrieved 23 August 2016. 
  8. ↑ 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. 
  9. ↑ 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. 
  10. ↑ "openBIS Change Log". Department of Biosystems Science and Engineering - ETHZ. 20 December 2013. https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log. Retrieved 02 March 2016. 
  11. ↑ 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. 
  12. ↑ Fuentes, J. (6 November 2014). "ELN-LIMS Project". ETH Zürich. pp. 15. Archived from the original on 23 August 2016. https://web.archive.org/web/20160823153756/https://wiki.systemsx.ch/download/attachments/91753082/Sybit%20ELN.pdf?version=1&modificationDate=1402649849499&api=v2. Retrieved 23 August 2016. 
  13. ↑ CISD Documentation Administrator (19 August 2016). "openBIS Change Log". Department of Biosystems Science and Engineering - ETHZ. Archived from the original on 23 August 2016. https://web.archive.org/web/20160823154943/https://wiki-bsse.ethz.ch/display/openBISDoc/openBIS+Change+Log. Retrieved 23 August 2016. 
  14. ↑ Franz-Josef, E. (18 May 2016). "openBIS Change Log - openBIS Documentation Rel. 16.05". Department of Biosystems Science and Engineering - ETHZ. https://wiki-bsse.ethz.ch/display/openBISDoc1605/openBIS+Change+Log. Retrieved 23 August 2016. 
  15. ↑ "openBIS ELN-LIMS for the Life Sciences". ETH Zürich. https://sis.id.ethz.ch/software/eln.html. Retrieved 23 August 2016. 
  16. ↑ "openBIS Setup Guide". Center for Information Science and Databases - ETHZ. 12 November 2020. https://unlimited.ethz.ch/display/openBISDoc2010/openBIS+setup+guide. Retrieved 04 May 2021. 
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