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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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Versioning


No version available

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 citations

 (11)
library_books

Abstracts from the 20th International Symposium on Signal Transduction at the Blood Brain Barriers

2017
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 […]

library_books

Jenkins CI, an Open Source Continuous Integration System, as a Scientific Data and Image Processing Platform

2016
SLAS Discov
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 […]

library_books

A Genome Wide siRNA Screen Implicates Spire1/2 in SipA Driven Salmonella Typhimurium Host Cell Invasion

2016
PLoS One
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, […]

library_books

Proteome wide association studies identify biochemical modules associated with a wing size phenotype in Drosophila melanogaster

2016
Nat Commun
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 […]

library_books

The FAIR Guiding Principles for scientific data management and stewardship

2016
Sci Data
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 […]

library_books

Large scale inference of protein tissue origin in gram positive sepsis plasma using quantitative targeted proteomics

2016
Nat Commun
PMCID: 4729823
PMID: 26732734
DOI: 10.1038/ncomms10261

[…] ms and ms/ms with ion accumulation times of 100 ms (ms) and 120 ms (ms/ms). the obtained raw files were converted to mzxml using the software tool proteowizard., data were stored and managed using openbis and all computational workflows were executed and managed using iportal. data integration, visualization and interpretation were done using ddb. the shotgun data were analysed as described […]


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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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