Dataset Information

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.

ABSTRACT:

Background

Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidly begin interpretation of large data sets collected for a system of interest. BioNetBuilder is an open-source client-server Cytoscape plugin that automatically integrates molecular interactions from all major public interaction databases and serves them directly to the user's Cytoscape environment. Until recently however, chicken and other eukaryotic model systems had little interaction data available.

Results

Version 2.0 of BioNetBuilder includes a redesigned synonyms resolution engine that enables transfer and integration of interactions across species; this engine translates between alternate gene names as well as between orthologs in multiple species. Additionally, BioNetBuilder is now implemented to be part of the Gaggle, thereby allowing seamless communication of interaction data to any software implementing the widely used Gaggle software. Using BioNetBuilder, we constructed a chicken interactome possessing 72,000 interactions among 8,140 genes directly in the Cytoscape environment. In this paper, we present a tutorial on how to do so and analysis of a specific use case.

Conclusion

BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/.

SUBMITTER: Konieczka JH

PROVIDER: S-EPMC2966329 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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Publications

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.

Konieczka Jay H JH Drew Kevin K Pine Alex A Belasco Kevin K Davey Sean S Yatskievych Tatiana A TA Bonneau Richard R Antin Parker B PB

BMC genomics 20090714

<h4>Background</h4>Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidly begin interpretation of large data sets collected for a system of interest. BioNetBuilder is an open-source client-server Cytoscape plugin that automatically integrates molecular interactions from all major public interaction databases and serves them directly to the us ...[more]

PMID: 19607657

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Dataset Information

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.

Background

Results

Conclusion

Publications

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.

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