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Open Access Highly Accessed Software

DIPSBC - data integration platform for systems biology collaborations

Felix Dreher1*, Thomas Kreitler1, Christopher Hardt1, Atanas Kamburov1, Reha Yildirimman1, Karl Schellander2, Hans Lehrach1, Bodo MH Lange1 and Ralf Herwig1*

Author Affiliations

1 Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany

2 Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany

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BMC Bioinformatics 2012, 13:85  doi:10.1186/1471-2105-13-85

Published: 8 May 2012

Abstract

Background

Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays. XML has become the most prominent format for representing and exchanging these data. However, besides the development of standards there is still a fundamental lack of data integration systems that are able to utilize these exchange formats, organize the data in an integrative way and link it with applications for data interpretation and analysis.

Results

We have developed DIPSBC, an interactive data integration platform supporting collaborative research projects, based on Foswiki, Solr/Lucene, and specific helper applications. We describe the main features of the implementation and highlight the performance of the system with several use cases. All components of the system are platform independent and open-source developments and thus can be easily adopted by researchers. An exemplary installation of the platform which also provides several helper applications and detailed instructions for system usage and setup is available at http://dipsbc.molgen.mpg.de webcite.

Conclusions

DIPSBC is a data integration platform for medium-scale collaboration projects that has been tested already within several research collaborations. Because of its modular design and the incorporation of XML data formats it is highly flexible and easy to use.

Keywords:
Data integration; XML; Data visualization