openBIS: a flexible framework for managing and analyzing complex data in biology research

BMC Bioinformatics

Software

Andreas Quandt¹  Lars Malmström¹  Ruedi Aebersold²  Piotr Buczek³  Izabela Adamczyk³  Angela Bauch³  Tomasz Pylak⁴  Bernd Rinn⁴  Kaloyan Enimanev⁴  Pawel Glyzewski⁴  Chandrasekhar Ramakrishnan⁴  Manuel Kohler⁴  Franz-Josef Elmer⁴  Christian Beisel⁵ 

[1] Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland;Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland;Faculty of Science, University of Zurich, Switzerland;Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland;Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland;Swiss Institute of Bioinformatics (SIB), Switzerland;Department of Biosystems Science and Engineering, Quantitative Genomics Facility, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland;

关键词: File System;    Data Space;    Application Server;    Bulk Data;    Metadata File;   

DOI  :  10.1186/1471-2105-12-468

 received in 2011-09-06, accepted in 2011-12-08,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundModern 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.ResultsWe 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.ConclusionsopenBIS 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.

【 授权许可】

Unknown   
© Bauch et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.