TY - JOUR
T1 - Network portal
T2 - A database for storage, analysis and visualization of biological networks
AU - Turkarslan, Serdar
AU - Wurtmann, Elisabeth J.
AU - Wu, Wei Ju
AU - Jiang, Ning
AU - Bare, J. Christopher
AU - Foley, Karen
AU - Reiss, David J.
AU - Novichkov, Pavel
AU - Baliga, Nitin S.
N1 - Funding Information:
Funding for open access charge: Enabling a Systems Biology Knowledgebase with Gaggle and Firegoose [DE-FG02-04ER63807]; ENIGMA, Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory (Office of Science, Office of Biological and Environmental Research of the US Department of Energy under Contract No. DE-AC02-05CH11231).
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84891759030
U2 - 10.1093/nar/gkt1190
DO - 10.1093/nar/gkt1190
M3 - Article
C2 - 24271392
AN - SCOPUS:84891759030
SN - 0305-1048
VL - 42
SP - D184-D190
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -