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.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
- Barillari, Caterina; Ottoz, Diana S.M.; Fuentes-Serna, Juan M.; Ramakrishnan, Chandrasekhar; Rinn, Bernd; Rudolf, Fabian (2016). "openBIS ELN-LIMS: An open-source database for academic laboratories". Bioinformatics 32 (4): 638–640. doi:10.1093/bioinformatics/btv606. PMC PMC4743625. PMID 26508761. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743625.
- 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 source code
- openBIS master documentation
- openBIS user documentation
- openBIS admin documentation
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 4.2 "Data Management Software Platform openBIS". ETH Zürich. https://sis.id.ethz.ch/software/openbis.html. Retrieved 23 August 2016.
- ↑ 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.
- ↑ "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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ "openBIS ELN-LIMS for the Life Sciences". ETH Zürich. https://sis.id.ethz.ch/software/eln.html. Retrieved 23 August 2016.
- ↑ "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.
