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openBIS specifications

Information


Unique identifier OMICS_01009
Name openBIS
Alternative names open Biology Information System, openBUS ELN-LIMS
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes

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Maintainers


  • person_outline Bernd Rinn <>
  • person_outline Fabian Rudolf <>

Additional information


https://wiki-bsse.ethz.ch/display/bis/Home Webinars https://openbis-eln-lims.ethz.ch/index.php/webinars/ Tutoriels https://openbis-eln-lims.ethz.ch/index.php/tutorials/

Publications for open Biology Information System

openBIS in publications

 (11)
PMCID: 5667590
DOI: 10.1186/s12987-017-0071-4

[…] (mainly rna-seq) (iii) to implement data-mining tools and (iv) to provide the data to both researchers and general public. for the implementation of the bbbhub, we will use the frame work “openbis”, an open source platform for managing scientific information, as its backbone. furthermore, we are developing an easy-to-use front-end system to allow all researchers to use it independently […]

PMCID: 5322829
PMID: 27899692
DOI: 10.1177/1087057116679993

[…] workflow, it should be noted that a number of similar tools designed to facilitate the design and execution of bioinformatics and imaging workflows already exist. for example, galaxy, taverna, openbis, loni, and knime have all been previously described. each of these systems has unique advantages and disadvantages that require careful consideration before a suitable workflow platform […]

PMCID: 5023170
PMID: 27627128
DOI: 10.1371/journal.pone.0161965

[…] cytoskeleton (dy-547-phalloidin) and the gfp-expressing bacteria (pm975)., all data that were generated during infectx related screens including raw and processed image data were shared through the openbis biology information system []. to achieve an efficient automated image-analysis pipeline applicable to the distinct screening features exploited by the pathogens of the infectx consortium, […]

PMCID: 5025782
PMID: 27582081
DOI: 10.1038/ncomms12649

[…] targeted swath extraction as described by schubert et al.. with the spectral library in hand, swath files are analysed using openswath implemented in the iportal gui. search results are stored in openbis file server system. exact parameters of the informatics swath workflow are given in the ., the peptide abundance was quantified using the area under the curves summing up co-eluting […]

PMCID: 4792175
PMID: 26978244
DOI: 10.1038/sdata.2016.18

[…] to search the data, access the metadata and download the data files, using a token to grant access when data files are restricted (‘a’)., fairdom (http://fair-dom.org/about): integrates the seek and openbis platforms to produce a fair data and model management facility for systems biology. individual research assets (or aggregates of data and models) are identified with unique and persistent […]


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openBIS institution(s)
ETH Zurich ID SIS and Swiss Institute of Bioinformatics, Zurich, Switzerland; ETH Zurich D-BSSE and Swiss Institute of Bioinformatics, Basel, Switzerland; Life Science Zurich PhD Program on Molecular and Translational Biomedicine and Competence Center for Personalized Medicine, Zurich, Switzerland
openBIS funding source(s)
Funded by the ETH Zurich.

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