title: Network portal: a database for storage, analysis and visualization of biological networks.
abstract: The ease of generating high-throughput data has enabled investigations into organismal complexity at the systems level through the inference of networks of interactions among the various cellular components (genes, RNAs, proteins and metabolites). The wider scientific community, however, currently has limited access to tools for network inference, visualization and analysis because these tasks often require advanced computational knowledge and expensive computing resources. We have designed the network portal (http://networks.systemsbiology.net) to serve as a modular database for the integration of user uploaded and public data, with inference algorithms and tools for the storage, visualization and analysis of biological networks. The portal is fully integrated into the Gaggle framework to seamlessly exchange data with desktop and web applications and to allow the user to create, save and modify workspaces, and it includes social networking capabilities for collaborative projects. While the current release of the database contains networks for 13 prokaryotic organisms from diverse phylogenetic clades (4678 co-regulated gene modules, 3466 regulators and 9291 cis-regulatory motifs), it will be rapidly populated with prokaryotic and eukaryotic organisms as relevant data become available in public repositories and through user input. The modular architecture, simple data formats and open API support community development of the portal.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Serdar
authors.initials: S
authors.lastname: Turkarslan
authors.forename: Elisabeth J
authors.initials: EJ
authors.lastname: Wurtmann
authors.forename: Wei-Ju
authors.initials: WJ
authors.lastname: Wu
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Bare
authors.forename: Karen
authors.initials: K
authors.lastname: Foley
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: Pavel
authors.initials: P
authors.lastname: Novichkov
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D003196:Computer Graphics; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020407:Internet; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors