openBIS
 | |
| Developer(s) | Scientific IT Services - 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 | https://openbis-eln-lims.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, every two weeks.[9] 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.[10]. The ELN plugin is now included in the openBIS 16.05 installer.
Features
- 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 9.1 or higher (with database superuser privileges)
- Java 1.6 or higher
Videos, screenshots, and other media
Numerous videos for openBIS can be found on the openBIS website.
Webinars for the openBIS ELN-LIMS can be found on the openBIS ELN-LIMS 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
- research groups at ETH
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. PMC PMC3275639. PMID 22151573. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275639.
External links
- openBIS wiki
- openBIS Sprint documentation
- openBIS 16.05 release documentation
- openBIS ELN-LIMS
- openBIS setup guide
- Old openBIS site
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.
- ↑ 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.
- ↑ "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.
- ↑ 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.
- ↑ "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.
