Cytoscape is an Open Source bioinformatics environment for biological network analysis, visualization, and modeling. It has grown to become a standard resource in academia and industry, due mainly to its timeliness (it was one of the first tools for visualization of biological networks), open development model (it is still one of few such tools that is open-source), and public plug-in interface (which allows anyone to add functionality to Cytoscape and has attracted many third-party developers and industrial partners). The NIH has funded Cytoscape development since 2004 under the program """"""""Continued Maintenance and Development of Software"""""""" (R01-GM070743). In this competitive renewal, we propose to continue to improve, maintain, and support Cytoscape along three Specific Aims. First, we will fit Cytoscape with a modular architecture using the OSGi framework ( OSGi will enable command-line and scripting interfaces, deployment of Cytoscape as a web-server, parallelization within cluster computing environments, and customization by different user communities. Second, we will develop a collection of new network visualization and analysis features organized around target Cytoscape workflows-i.e., sets of both novel and commonly-used operations chained together to form analysis pipelines. The new features (including new data services, a more powerful structure for network attributes, and a unified network query engine) will greatly enhance the accessibility of complex but powerful network analysis operations to a broad experimental and clinical research community, and they will enable new uses of network biology in the study of human disease. Third, we will invest significant resources in outreach, training, and community support through development of education and training programs, bolstering collaborations with existing data and tool providers, and implementation of measures to actively reach out to attract new users and collaborators. Cytoscape is an important milepost on the road to developing large-scale """"""""circuit diagrams"""""""" of the cell. Continued support of Cytoscape will allow other laboratories to avoid reinventing the same tools, time that can instead be devoted to more complex analyses or to basic research.

Public Health Relevance

Cytoscape has supported hundreds of publications involving biological network analysis, and major databases rely on Cytoscape for visualization and analysis of molecular interactions. Renewed funding of Cytoscape will be crucial to maintain a strong core software environment and to expand its function to meet current and future challenges such as network-based disease diagnostics and interpretation of genotypes.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BST-Q (01))
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Brazhnik, Paul
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University of California San Diego
Engineering (All Types)
Schools of Arts and Sciences
La Jolla
United States
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Marcotte, Richard; Sayad, Azin; Brown, Kevin R et al. (2016) Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance. Cell 164:293-309
Franz, Max; Lopes, Christian T; Huck, Gerardo et al. (2016) Cytoscape.js: a graph theory library for visualisation and analysis. Bioinformatics 32:309-11
Summer, Georg; Kelder, Thomas; Ono, Keiichiro et al. (2015) cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics 31:3868-9
Pratt, Dexter; Chen, Jing; Welker, David et al. (2015) NDEx, the Network Data Exchange. Cell Syst 1:302-305
Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi et al. (2015) CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res 4:478
Liu, Ying; Sen, Sanjana; Wannaiampikul, Sivaporn et al. (2015) Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action. Biochem J 469:71-82
Kramer, Michael; Dutkowski, Janusz; Yu, Michael et al. (2014) Inferring gene ontologies from pairwise similarity data. Bioinformatics 30:i34-42
Welker, David; Demchak, Barry (2014) Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Res 3:150
Giovannetti, Elisa; Wang, Qiuyan; Avan, Amir et al. (2014) Role of CYB5A in pancreatic cancer prognosis and autophagy modulation. J Natl Cancer Inst 106:djt346
Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael et al. (2014) NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res 42:D1269-74

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