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


CONCLUSIONS
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/.
Konieczka
Jay H
JH
Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA. jayk@u.arizona.edu.
Drew
Kevin
K
Pine
Alex
A
Belasco
Kevin
K
Davey
Sean
S
Yatskievych
Tatiana A
TA
Bonneau
Richard
R
Antin
Parker B
PB
D000818:Animals; D002645:Chickens / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D023281:Genomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D049490:Systems Biology