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 oe of few such tools that is open-source), and public plug-in/Apps interface (allowing anyone to add functionality to Cytoscape and attracting many third-party developers and industrial partners). The NIH has funded Cytoscape development since 2004 under the program """"""""Continued Development and Maintenance of Software"""""""" (R01-GM070743). In this competitive renewal, we will improve, maintain, and support Cytoscape along three Specific Aims. First, we will develop new Cytoscape infrastructure for relating networks across conditions, times, species, and a hierarchy of scales. This infrastructure will be used to implement end-user tools for network comparison and differential analysis, for identifying and visualizing hierarchical network structures, and for aligning these hierarchies against references such as the Gene Ontology. Second, we will work to expand the Cytoscape User Experience (UX), with a focus on improved speed of analysis and display, standardizing and automating common workflows, and collaborative data sharing over the web. This work will take advantage of the latest computing technologies including multi-core processors, distributed computing environments / clouds, general purpose GPU computing, and graph databases. Third, we will continue to maintain and disseminate the Cytoscape code base, including bug tracking / fixing;CPU and memory profiling and optimization;and web-based software distribution of stable and development versions. Also, we will promote new App development through social coding paradigms such as GitHub. 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

Continued support of Cytoscape will allow NIH investigators to maintain and magnify their ongoing successful efforts to mine molecular networks for new pathways, biomarkers, and individual variations underlying disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Brazhnik, Paul
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
Zip Code
Tong, Jiefei; Helmy, Mohamed; Cavalli, Florence M G et al. (2017) Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics 17:
Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique et al. (2017) Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML. Blood 129:2657-2666
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
Wojtowicz, Edyta E; Lechman, Eric R; Hermans, Karin G et al. (2016) Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors. Cell Stem Cell 19:383-96
Torchia, Jonathon; Golbourn, Brian; Feng, Shengrui et al. (2016) Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell 30:891-908
Summer, Georg; Kelder, Thomas; Ono, Keiichiro et al. (2015) cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics 31:3868-9
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
Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi et al. (2015) CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res 4:478
Pratt, Dexter; Chen, Jing; Welker, David et al. (2015) NDEx, the Network Data Exchange. Cell Syst 1:302-305

Showing the most recent 10 out of 49 publications