title: openBIS: a flexible framework for managing and analyzing complex data in biology research.
abstract: BACKGROUND
  Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.
  
  
  RESULTS
  We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.
  
  
  CONCLUSIONS
  openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.
authors.affiliation: Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland.
authors.forename: Angela
authors.initials: A
authors.lastname: Bauch
authors.forename: Izabela
authors.initials: I
authors.lastname: Adamczyk
authors.forename: Piotr
authors.initials: P
authors.lastname: Buczek
authors.forename: Franz-Josef
authors.initials: FJ
authors.lastname: Elmer
authors.forename: Kaloyan
authors.initials: K
authors.lastname: Enimanev
authors.forename: Pawel
authors.initials: P
authors.lastname: Glyzewski
authors.forename: Manuel
authors.initials: M
authors.lastname: Kohler
authors.forename: Tomasz
authors.initials: T
authors.lastname: Pylak
authors.forename: Andreas
authors.initials: A
authors.lastname: Quandt
authors.forename: Chandrasekhar
authors.initials: C
authors.lastname: Ramakrishnan
authors.forename: Christian
authors.initials: C
authors.lastname: Beisel
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Bernd
authors.initials: B
authors.lastname: Rinn
mesh_terms: D023281:Genomics; D019451:Information Management / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods; D055432:Metabolomics; D012984:Software; D013223:Statistics as Topic; D049490:Systems Biology / Q000379:methods*