DIPSBC--data integration platform for systems biology collaborations.

BMC Bioinformatics
Felix DreherRalf Herwig

Abstract

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. 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 whi...Continue Reading

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Citations

Oct 11, 2012·Briefings in Bioinformatics·Wasco WruckChristian R A Regenbrecht
Jul 15, 2015·BMC Systems Biology·Katherine WolstencroftCarole Goble
Apr 3, 2019·BMC Bioinformatics·Wei GuUNKNOWN IMI OncoTrack and the IMI eTRIKS consortia

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Datasets Mentioned

BETA
GSE3325

Methods Mentioned

BETA
PCR
chip
two-hybrid

Software Mentioned

PRIDE
MI
ISAcreator
BioModels
mzData viewer
Perl
R
mzData
ConsensusPathDB
Genome Browser

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