Cytoscape 2.8: new features for data integration and network visualization

By Michael E. Smoot, Keiichiro Ono, Johannes Ruscheinski, Trey Ideker. Bioinform., 2010

2,130 citations recorded by the source corpus.

Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. Availability and implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org. Contact: msmoot@ucsd.edu

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0e6aefc52cc98104fdd802cd4fa9878d9f5fbca5

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In Biophysics

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Citations in the corpus

PathVisio 3: An Extendable Pathway Analysis Toolbox (2015, neutral): “Cytoscape is a popular network analysis and visualization tool [29] and the WikiPathways app allows users to load pathways as networks in Cytoscape to perform network analysis.”
SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics (2019, neutral): “The latter can be imported in tools such as Cytoscape (45).”
Network-based stratification of tumor mutations (2013, positive): “This set of genes was projected onto the HumanNet network and visualized using Cytoscape 35 .”
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. (2013, positive): “biological processes using Gene Ontology annotations, and networks were visualized in Cytoscape (Smoot et al., 2011).”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, positive): “Name Content Website References KEGG Metabolic pathway resource http://kegg.jp Kanehisa et al., 2012 MetaCyc http://metacyc.org Caspi et al., 2012 HumanCyc http://humancyc.org Romero et al., 2005 SMPDB Small Molecule (e.g., drug) Pathway Database http://smpdb.ca Frolkis et al., 2010 HMDB Human Metab”
Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges (2013, positive): “In addition to molecules, we have implemented a 3D visualization of biological networks from Cytoscape [17] where the depth can be adapted to avoid overlap between different nodes.”