Universität Basel Universität Zürich Swiss Institute of Bioinformatics ETH Zurich École Polytechnique Fédérale de Lausanne  Friedrich Miescher Institute for Biomedical Research

openBIS

openBIS is an open (and if needed distributed) framework for managing and sharing different types of biological information. Its main purpose is 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.

The openBIS software framework can be easily extended and has been customized for various technologies, among them

  • high content screening and imaging,
  • genomics,
  • proteomics,
  • metabolomics,
  • flow cytometry,
  • general lab information.

openBIS features:

  • A modern web-based user-interface.
  • A data browser for tablet computers.
  • A fast search function for all metadata.
  • A set of back-end features for "heavy data lifting", including support for automatic checksumming of new data, continuous archiving and adding / removing new file shares as needed.
  • Full support for "data provenance tracking" by storing the relationships between data sets and samples in graphs and keeping the history of metadata.
  • A concise Application Programming Interface based on open web standards.
  • Many plugin interfaces to extend its functionality, e.g. for data validation, for data ingestion via programmable "dropbox scripts" and for small and focused "web apps".
  • Integration into KNIME Workflow Application.



Short facts

  • Developed and supported by the Center for Information Sciences and Databases (D-BSSE - ETH Zürich).
  • Server runs on Linux and other POSIX systems.
  • Productively used by research labs, facilities, consortia and life science companies in Switzerland, Europe and the USA.

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Contacts


E-mail: sybit(at)sympa.systemsx.ch | Wiki: SyBIT Wiki
Copyright © 2012,SyBIT - SystemsX.ch Biology IT.

E-mail: sybit(at)sympa.systemsx.ch
Wiki: SyBIT Wiki
Copyright © 2012,SyBIT - SystemsX.ch Biology IT.